rs17307677

Positions:

• chrY-16050954-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;