rs9658630

Positions:

• chr14-92922133-C-T

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 152,094 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.777

Gnomad4 AMR AF: 0.800

Gnomad4 ASJ AF: 0.728

Gnomad4 EAS AF: 0.948

Gnomad4 SAS AF: 0.825

Gnomad4 FIN AF: 0.728

Gnomad4 NFE AF: 0.759

Gnomad4 OTH AF: 0.783

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9658630; hg19: chr14-93388478;