rs9658630

Variant names:

• chr14-92922133-C-T
• rs9658630

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 152,094 control chromosomes in the GnomAD database, including 45,733 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 (45733 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• 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: 117597 AN: 151976 Hom.: 45706 Cov.: 31

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.676

Gnomad AMR AF: 0.801

Gnomad ASJ AF: 0.728

Gnomad EAS AF: 0.948

Gnomad SAS AF: 0.827

Gnomad FIN AF: 0.728

Gnomad MID AF: 0.854

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: 117675 AN: 152094 Hom.: 45733 Cov.: 31 AF XY: 0.775 AC XY: 57593 AN XY: 74350

African (AFR) AF: 0.777 AC: 32232 AN: 41476

American (AMR) AF: 0.800 AC: 12239 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.728 AC: 2527 AN: 3470

East Asian (EAS) AF: 0.948 AC: 4898 AN: 5166

South Asian (SAS) AF: 0.825 AC: 3979 AN: 4822

European-Finnish (FIN) AF: 0.728 AC: 7695 AN: 10570

Middle Eastern (MID) AF: 0.853 AC: 249 AN: 292

European-Non Finnish (NFE) AF: 0.759 AC: 51588 AN: 67986

Other (OTH) AF: 0.783 AC: 1654 AN: 2112

Alfa AF: 0.754 Hom.: 5390

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	-0.92
CADD	Benign	0.14
DANN	Benign	0.49
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs9658630; hg19: chr14-93388478;