rs9658631

Variant names:

• chr14-92922159-G-T
• rs9658631

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.774 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

Gnomad4 AFR AF: 0.777

Gnomad4 AMR AF: 0.800

Gnomad4 ASJ AF: 0.727

Gnomad4 EAS AF: 0.948

Gnomad4 SAS AF: 0.825

Gnomad4 FIN AF: 0.727

Gnomad4 NFE AF: 0.759

Gnomad4 OTH AF: 0.782

Alfa AF: 0.755 Hom.: 5600

Bravo AF: 0.775

Asia WGS AF: 0.883 AC: 3071 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9658631; hg19: chr14-93388504;