rs17315835

Variant names:

• chrY-17067455-T-C
• rs17315835

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.049 (0 hom., 1624 hem., cov: 0)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0440
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.124 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0489 AC: 1623 AN: 33222 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0107

Gnomad AMI AF: 0.0798

Gnomad AMR AF: 0.0806

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.000797

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.000904

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.0483

Gnomad OTH AF: 0.128

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0488 AC: 1624 AN: 33287 Hom.: 0 Cov.: 0 AF XY: 0.0488 AC XY: 1624 AN XY: 33287

African (AFR) AF: 0.0107 AC: 92 AN: 8613

American (AMR) AF: 0.0804 AC: 289 AN: 3594

Ashkenazi Jewish (ASJ) AF: 0.360 AC: 279 AN: 776

East Asian (EAS) AF: 0.000797 AC: 1 AN: 1254

South Asian (SAS) AF: 0.140 AC: 203 AN: 1452

European-Finnish (FIN) AF: 0.000904 AC: 3 AN: 3320

Middle Eastern (MID) AF: 0.377 AC: 26 AN: 69

European-Non Finnish (NFE) AF: 0.0484 AC: 656 AN: 13549

Other (OTH) AF: 0.130 AC: 58 AN: 447

Alfa AF: 0.670 Hom.: 1379

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	6.2
DANN	Benign	0.24
PhyloP100		-0.044

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs17315835; hg19: chrY-19179335;