rs9658631

Variant names:

• chr14-92922159-G-T
• rs9658631

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.774 in 152,020 control chromosomes in the GnomAD database, including 45,703 homozygotes. 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 0.77 (45703 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.174
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.926 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: 0.774 AC: 117525 AN: 151902 Hom.: 45675 Cov.: 31

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.675

Gnomad AMR AF: 0.801

Gnomad ASJ AF: 0.727

Gnomad EAS AF: 0.948

Gnomad SAS AF: 0.827

Gnomad FIN AF: 0.727

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.759

Gnomad OTH AF: 0.781

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

GnomAD4 genome AF: 0.774 AC: 117604 AN: 152020 Hom.: 45703 Cov.: 31 AF XY: 0.774 AC XY: 57544 AN XY: 74312

African (AFR) AF: 0.777 AC: 32226 AN: 41458

American (AMR) AF: 0.800 AC: 12240 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.727 AC: 2522 AN: 3468

East Asian (EAS) AF: 0.948 AC: 4885 AN: 5152

South Asian (SAS) AF: 0.825 AC: 3969 AN: 4810

European-Finnish (FIN) AF: 0.727 AC: 7675 AN: 10556

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.759 AC: 51571 AN: 67968

Other (OTH) AF: 0.782 AC: 1651 AN: 2110

Alfa AF: 0.768 Hom.: 57367

Bravo AF: 0.775

Asia WGS AF: 0.883 AC: 3071 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.4
DANN	Benign	0.49
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs9658631; hg19: chr14-93388504;