rs17315926

Variant names:

• chrY-17263414-C-T
• rs17315926

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0604 AC: 1949 AN: 32283 Hom.: 0 Cov.: 0 AF XY: 0.0604 AC XY: 1949 AN XY: 32283

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

Gnomad4 AFR AF: 0.00986

Gnomad4 AMR AF: 0.00675

Gnomad4 ASJ AF: 0.0785

Gnomad4 EAS AF: 0.00327

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.0364

Gnomad4 NFE AF: 0.0911

Gnomad4 OTH AF: 0.0442

Alfa AF: 0.560 Hom.: 70

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17315926; hg19: chrY-19375294;