Y-16050954-T-C

Variant names:

• chrY-16050954-T-C
• rs17307677

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 0.056 (0 hom., 1876 hem., cov: 0)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.260
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0564 AC: 1875 AN: 33227 Hom.: 0 Cov.: 0

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

African (AFR) AF: 0.00969 AC: 84 AN: 8665

American (AMR) AF: 0.00544 AC: 20 AN: 3677

Ashkenazi Jewish (ASJ) AF: 0.0777 AC: 60 AN: 772

East Asian (EAS) AF: 0.00246 AC: 3 AN: 1218

South Asian (SAS) AF: 0.285 AC: 411 AN: 1444

European-Finnish (FIN) AF: 0.0283 AC: 97 AN: 3424

Middle Eastern (MID) AF: 0.0278 AC: 2 AN: 72

European-Non Finnish (NFE) AF: 0.0883 AC: 1177 AN: 13332

Other (OTH) AF: 0.0359 AC: 17 AN: 474

Alfa AF: 0.0658 Hom.: 501

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.0
DANN	Benign	0.73
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs17307677; hg19: chrY-18162834;