rs17307677

Variant names:

• chrY-16050954-T-C
• rs17307677

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 0.056 (0 hom., 1876 hem., cov: 0)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.260

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.262 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: 0.0564 AC: 1875 AN: 33227 Hom.: 0 Cov.: 0 AF XY: 0.0564 AC XY: 1875 AN XY: 33227

Gnomad AFR AF: 0.00975

Gnomad AMI AF: 0.0233

Gnomad AMR AF: 0.00545

Gnomad ASJ AF: 0.0777

Gnomad EAS AF: 0.00246

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.0283

Gnomad MID AF: 0.0274

Gnomad NFE AF: 0.0883

Gnomad OTH AF: 0.0362

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

GnomAD4 genome AF: 0.0563 AC: 1876 AN: 33293 Hom.: 0 Cov.: 0 AF XY: 0.0563 AC XY: 1876 AN XY: 33293

Gnomad4 AFR AF: 0.00969

Gnomad4 AMR AF: 0.00544

Gnomad4 ASJ AF: 0.0777

Gnomad4 EAS AF: 0.00246

Gnomad4 SAS AF: 0.285

Gnomad4 FIN AF: 0.0283

Gnomad4 NFE AF: 0.0883

Gnomad4 OTH AF: 0.0359

Alfa AF: 0.107 Hom.: 470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.0
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17307677; hg19: chrY-18162834;