rs10933964

Variant names:

• chr3-108820344-A-G
• rs10933964

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.388 in 151,178 control chromosomes in the GnomAD database, including 12,839 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 0.39 (12839 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00100

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.495 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: 0.389 AC: 58688 AN: 151058 Hom.: 12833 Cov.: 31

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.388 AC: 58692 AN: 151178 Hom.: 12839 Cov.: 31 AF XY: 0.387 AC XY: 28539 AN XY: 73776

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.416

Gnomad4 ASJ AF: 0.496

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.373

Gnomad4 FIN AF: 0.512

Gnomad4 NFE AF: 0.499

Gnomad4 OTH AF: 0.395

Alfa AF: 0.425 Hom.: 2178

Bravo AF: 0.369

Asia WGS AF: 0.243 AC: 850 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
CADD	Benign	16
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10933964; hg19: chr3-108539191;