rs17315926

Variant names:

• chrY-17263414-C-T
• rs17315926

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 0.060 (0 hom., 1948 hem., cov: 0)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.594
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.283 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: 0.0604 AC: 1949 AN: 32283 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00992

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.00676

Gnomad ASJ AF: 0.0785

Gnomad EAS AF: 0.00327

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.0364

Gnomad MID AF: 0.0278

Gnomad NFE AF: 0.0911

Gnomad OTH AF: 0.0443

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

GnomAD4 genome AF: 0.0602 AC: 1948 AN: 32342 Hom.: 0 Cov.: 0 AF XY: 0.0602 AC XY: 1948 AN XY: 32342

African (AFR) AF: 0.00986 AC: 83 AN: 8417

American (AMR) AF: 0.00675 AC: 23 AN: 3407

Ashkenazi Jewish (ASJ) AF: 0.0785 AC: 59 AN: 752

East Asian (EAS) AF: 0.00327 AC: 4 AN: 1224

South Asian (SAS) AF: 0.306 AC: 433 AN: 1413

European-Finnish (FIN) AF: 0.0364 AC: 115 AN: 3158

Middle Eastern (MID) AF: 0.0282 AC: 2 AN: 71

European-Non Finnish (NFE) AF: 0.0911 AC: 1205 AN: 13232

Other (OTH) AF: 0.0442 AC: 20 AN: 453

Alfa AF: 0.560 Hom.: 70

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.1
DANN	Benign	0.26
PhyloP100		-0.59

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: rs17315926; hg19: chrY-19375294;