My Y DNA Private Variants

I am shown to have 10 Private variants in Y Chromosome. I checked them in gnomAD browser. 9 of the 10 were found. All of those 9 have 1 person that has the variant, and they are all from the African/African American group. Y-4689310-A-T has a CADD score of 11.9, and it is an intergenic variant. The CADD score is quite high for an intergenic variant.

Y-13205377-C-G

Intergenic variant, Enhancer according to Encode

0.002988% (1 out of 33,470)

4.74

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

Y-13408427-T-C

Intronic variant (18 transcripts)

UTY ( (Ubiquitously Transcribed Tetratricopeptide Repeat Containing, Y-Linked)

https://www.genecards.org/cgi-bin/carddisp.pl?gene=UTY

0.00308% (1 out of 32,469)

5.07

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

Y-14386154-T-C

Intergenic variant

0.002982% (1 out of 33,529)

4.00

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

Y-16016460-G-C

Intergenic variant

0.002985% (1 out of 33,504)

1.63

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

Y-20620799-G-A

Intergenic variant

0.003023% (1 out of 33,081)

2.39

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

Y-26639245-G-A

A=0.00 (1 out of 15,951 (0,006 %) - GnomAD)

2.34

https://www.ncbi.nlm.nih.gov/snp/rs2090426010

Y-4689310-A-T

Intergenic

0.003051% (1 out of 32,780)

11.9

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

Y-6988012-G-A

Intronic variant (3 transcripts)

TBL1Y (Transducin Beta Like 1 Y-Linked)

https://www.genecards.org/cgi-bin/carddisp.pl?gene=TBL1Y

0.003008% (1 out of 33,249)

0.943

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

Y-7293460-A-G

Intronic variant (2 transcripts)

PRKY (Protein Kinase Y-Linked) pseudogene

https://www.genecards.org/cgi-bin/carddisp.pl?gene=PRKY

0.003188% (1 out of 31,372)

5.21

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

Y-7786073-C-T

Intronic variant (3 transcripts)

RFTN1P1 (Raft-Linking Protein Pseudogene)

https://www.genecards.org/cgi-bin/carddisp.pl?gene=RFTN1P1

0.003011% (1 out of 33,217)

0.195

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

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