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My Private Y DNA Variants Found in Other Men in gnomAD and AllOfUs

 I participated in AllOfUs Research back in August 2024 to contribute in any way to genomic research with the use of my DNA. Africans have the greatest genetic diversity of all the continental peoples on our planet Earth by far, but people of African ancestry make up a tiny proportion of the participants. The great under-representation of people of African ancestry one of the reasons why I want to help contribute. My other reason is that I want to help with research studies on neurological and neurodevelopmental issues with my having Ataxia, Dyslexia, Dyspraxia, ADHD.  

My wanting to contribute is the main reason that I did FamilyTreeDNA Big Y-700.  I already knew that I had an African Y DNA haplogroup after doing 23andme test and told that I had E2b1 and then later told E-M85. Only 1 in 1,500 23andme customers share my E-M85 haplogroup group assignment.

I did FamilyTreeDNA Big Y-700 Test, and I was assigned Y DNA haplogroup E-BY101982. Only six men are known to have the markers for E-BY101982 which formed in 850 CE, but I am the only one assigned to it. The five other men were assigned to haplogroups that are downstream of E-BY101982. E-CTS4257 is an upstream haplogroup of E-BY101982, and it was formed in 5450 BCE.  Globetrekker shows that it may have originated in South Sudan.  My earliest known ancestor on my paternal line is my 4th Great Grandfather John W. Daggs who was an enslaved African American born in Virginia and was not with his wife and their six children when they arrived in New Orleans from Alexandria, District of Columbia in 1835. My 2nd Great Grandfather William Henry Daggs Jr was both the first of my paternal line to be born free after American slavery ended and the first of my paternal line to use the last name Scott.  He didn't keep the last name, but his two sons did.  He was recorded as having a variation of Daggs including the French name Daigle in the 1870, 1880, 1900, 1910, 1920, 1930 US Censuses. My Great Grandfather Ivory Scott was the first of my patrilineal ancestors to permanently go by the last name Scott which passed down through my paternal line up to my father Lawrence Nolan Scott.  I was born with the last name Andrews (originally Andrade from the Cape Verde Islands which was a Portuguese colony until 1975), and I legally changed it to Scott in 2011.

In the last four years, I found out that I have two younger paternal half brothers. Through 23andme, I connected with a paternal half brother in 2022. Through AncestryDNA, I connected with my other paternal half brother in 2024. My paternal half brothers had different mothers and didn't know each other just like they neither knew me. None of us grew up knowing our father. I know that I share E-BY101982 Y DNA haplogroup with my two brothers.

FamilyTreeDNA shows that I have ten private Y DNA variants which are variants that are not shared between any branch members or which have not yet been validated and placed on the Haplotree.  I also found another one. I don't remember how I found it. I might have found one through my Dante Labs genomic data or my Sequencing genomic data. I got whole genome testing done through both those companies.

I searched for all eleven private variants in Genome Aggregation Database (gnomAD) which I always use when finding information about genomic variants of any kind.  Ten of them were found in just one man (in African/African American genetic group) in gnomAD, and he isn't me for I am not in that database.  Therefore, these variants are not private.  They're certainly not novel.  

I searched to see if any of the eleven Y DNA variants are found in other men in AllOfUs. All of the individuals in these genetic groups are Americans. In All of Us, “African” ,"East Asian,“European”,"Americas", "Middle Eastern", and "South Asian" refer to continental‑level genetic ancestry clusters based on allele‑frequency patterns and not to the participants’ identities, national origins, or race. These labels describe DNA similarity to reference populations and not who the people are. "Remaining" is a genetic group for individuals that do not neatly fit the patterns of any of the genetic ancestry groups that are displayed in AllOfUs. They may cluster with a different genetic ancestry group or they may not cluster fully with any group displayed in AllOfUs.

Ten of them were found in other men.

Five of them were found in only two men including one man in African genetic group and one in Remaining genetic group. I am in Remaining genetic group because I don't neatly fit into the African genetic group with my ancestry being nearly an even mix of Sub Saharan African and European.  My 23andme Ancestry Composition/Parental Inheritance has me as being 49.7% (43.4% paternal/6.3% maternal) Sub Saharan African, 47.5% (43.2% maternal/4.3% paternal) European, 1.7% (1.0% maternal/0.7% paternal) Indigenous American, 0.6% (all maternal) Northern West Asian, 0.3% (all paternal) Chinese/Southeast Asian, and 0.2% (all maternal) Unassigned.  

One of the variants was found in two men in the European genetic group and that definitely surprised me.  I thought all my variants would be found in only men in the African genetic group. E-BY101982 is an African Y DNA haplogroup.

There is only one variant not found in either gnomAD or AllOfUs.  It is not found in any other person in databases.  Therefore, it is my only variant that can be considered a private variant as well as a novel variant.

Looking at the variants from a Genomic perspective, ten of them involve Transcription Factors which are proteins that bind to DNA and regulates gene expression by promoting or suppressing transcription.  Two of them involve candidate cis-Regulatory Elements (cCREs) which are genomic regions identified by the ENCODE (Encyclopedia of DNA Elements) project that likely regulate gene expression, characterized by high chromatin accessibility, specific histone marks (H3K4me3, H3K27ac), and transcription factor binding. 

Transcription factor binding site changes were assessed with FABIAN. Only TFs with predicted binding gain (Δscore ≥ 0.70) or loss (Δscore ≤ −0.70) are reported.


my blog post about my Genealogical Ancestry

https://diversegenes.blogspot.com/2020/12/my-genealogical-ancestry.html


my blog post about my ethnic analyses from 7 DNA companies/sites

https://diversegenes.blogspot.com/2021/09/my-ethnic-analyses-ancestrydna-23andme.html


my previous Y DNA blog posts

https://diversegenes.blogspot.com/2022/01/my-y-dna-haplogroup-e-by71723.html

https://diversegenes.blogspot.com/2023/02/my-familytreedna-ydna-haplogroup-report.html

https://diversegenes.blogspot.com/2024/01/my-y-dna-haplogroup-variants-and.html

https://diversegenes.blogspot.com/2024/10/my-y-dna-private-variants.html


my blog posts about learning my Paternal Grandfather Nolan Scott's parentage and family history

https://diversegenes.blogspot.com/2023/01/ancestrydna-confirmation-of-carrie.html

https://diversegenes.blogspot.com/2023/02/learning-about-my-scott-family-of.html

https://diversegenes.blogspot.com/2023/03/my-paternal-2nd-great-grandmother.html

https://diversegenes.blogspot.com/2023/02/my-patrilineal-name-scott-changed-from.html

https://diversegenes.blogspot.com/2023/06/corrections-about-my-paternal.html

https://diversegenes.blogspot.com/2023/09/death-certificate-of-my-patrilineal.html

https://diversegenes.blogspot.com/2023/09/both-my-great-grandfather-ivory-scott.html

https://diversegenes.blogspot.com/2024/10/my-patrilineal-2nd-great-grandfather.html


novel  Y-26639245-G-A       private

Upstream variant in PARP41

Transcription Factor Binding site losses - ZNF148, ZFP57


Y-13205377-C-G   

Intergenic variant

1/33,470 (1 African/African American) gnomAD

2/208,544  (1 African, 1 Remaining) AllOfUs

Intergenic variant

https://gnomad.broadinstitute.org/variant/Y-13205377-C-G?dataset=gnomad_r4

https://databrowser.researchallofus.org/snvsindels/Y-13205377-C-G

Distal Enhancer

Distal Enhancer - GM2338 (skin cell line) in Core Collection

Transcription Factor - H1 (embryonic cell line) in Core Collection

Enhancer chromatin state in H1 (embryo)

Enhancer chromatin state in HUES64 (embryo)

Enhancer chromatin state in iPS DF 19.11 (skin)

Weak Trascirption chromatin state in iPS-20b (skin)

EP300 Transcription Factor Binding Site (37 experiments with H1 as biosample)

https://screen.wenglab.org/GRCh38/ccre/EH38E2775649

Transcription Factors - POU5F1, TP53, NANOG, JUN, TCF3, ETS1, EP300, SP1 (ReMap Atlas Of Regulatory Regions)

Transcription Factor Binding Site gains - ZNF343, MAF, HSF2, HSF1


Y-6988012-G-A 

Intron variant in TBL1Y

1/33,249 (African/African American) gnomAD

2/208,190 (1 African, 1 Remaining) AllOfUs

https://gnomad.broadinstitute.org/variant/Y-6988012-G-A?dataset=gnomad_r4

https://databrowser.researchallofus.org/snvsindels/Y-6988012-G-A

CA (Chromatin Accessibility)

Heterochromatin state in foreskin fibroblast (skin)

Heterochromatin state in mesenchymal stem cell (connective tissue)

endothelial cell of umbilical vein (blood vessell)

https://screen.wenglab.org/GRCh38/ccre/EH38E4533911

Transcription Factors - TP63, LDB1, TAL1, GATA1, KLF4 (ReMap Atlas of Regulatory Regions)

Transcription Factor Binding gains - HOX10, POU3F2, GFI1, PDX1, ZNF85, HOXC9

Transcription Facor Binding losses - GRHL1, TP63, GRHL2, SCRT1, SCRT2


Y-13408427-T-C 

Intergenic variant

1/33,470 (1 African/African American) gnomAD

3/208,221 (2 African, 1 Remaining) AllOfUs

https:/m/gnomad.broadinstitute.org/variant/Y-13408427-T-C?dataset=gnomad_r4

https://databrowser.researchallofus.org/snvsindels/Y-13408427-T-C

Transcription Factor Binding gains - FLI1, ETV2, ELF4, ELF1, ERG, SPIB, ERF, SPI1, IRF9, ELF5, ETV6, ELK1, EHF, STAT4


Y-7786073-C-T

Intron variant in RFTNP1

1/33,217 (African/African American) gnomAD

2/208,478 (1 African, 1 Remaining) AllOfUS

https://gnomad.broadinstitute.org/variant/Y-7786073-C-T?dataset=gnomad_r4

https://databrowser.researchallofus.org/snvsindels/Y-7786073-C-T

Transcription Factor Binding Sites gains - ATF7, CREB5, ATF2, NFIL3, NKX3-2

Transcription Factor Binding Sites losses - ZKSCAN5, RORC


Y-14386154-T-C 

1/33,529 (1 African/African American) gnomAD

https://gnomad.broadinstitute.org/variant/Y-14386154-T-C?dataset=gnomad_r4

Transcription Factor Binding Site gains - ZKSCAN1, ZNF416

Transcription Factor Binding Site losses - ZNF652, HNF1B, FOXG1


Y-4689310-A-T 

Intergenic variant

1/32,780  (1 African/African American) gnomAD

14/207,874 (10 African, 2 Remaining) AllOfUs

https://gnomad.broadinstitute.org/variant/Y-4689310-A-T?dataset=gnomad_r4

https://databrowser.researchallofus.org/snvsindels/Y-4689310-A-T

Transcription Factor Binding Site losses - CUX2, HOXB4


Y-16016460-G-C 

Intergenic variant

1/33,504 (1 African/American) gnomAD

5/208,653 (2 African, 2 European, 1 Remaining) AllOfUs

https://gnomad.broadinstitute.org/variant/Y-16016460-G-C?dataset=gnomad_r4

https://databrowser.researchallofus.org/snvsindels/Y-16016460-G-C

Transcription Factor Binding Sites gains - ZNF708

Transcription Factor Binding Site losses - TBX19


Y-20620799-G-A 

Intergenic variant

1/33,081 (1 African/African American) gnomAD

2/208,331 (1 African, 1 Remaining) AllOfUs

https://gnomad.broadinstitute.org/variant/Y-20620799-G-A?dataset=gnomad_r4

https://databrowser.researchallofus.org/snvsindels/Y-20620799-G-A

Transcription Factor Binding Site losses - ZNF136


Y-20620799-G-A 

Intergenic variant

1/33,081 (1 African/African American) gnomAD

2/208,311 (1 African, 1 Remaining) AllOfUS

https://gnomad.broadinstitute.org/variant/Y-20620799-G-A?dataset=gnomad_r4

https://databrowser.researchallofus.org/snvsindels/Y-20620799-G-A

Transcription Factor Binding Site losses - ZNF136


Y-7293460-A-G 

Intron variant in PRKY

1/31,372 (1 African/African American) gnomAD

2/208,105 (1 African, 1 Remaining) AllOfUs

https://gnomad.broadinstitute.org/variant/Y-7293460-A-G?dataset=gnomad_r4

https://databrowser.researchallofus.org/snvsindels/Y-7293460-A-G








 

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