rs10931041

Variant names:

• chr2-182820835-C-T
• rs10931041

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 0.531 in 152,028 control chromosomes in the GnomAD database, including 21,882 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 0.53 (21882 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.238
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.576 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: 0.531 AC: 80736 AN: 151910 Hom.: 21858 Cov.: 32

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.520

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.531 AC: 80798 AN: 152028 Hom.: 21882 Cov.: 32 AF XY: 0.529 AC XY: 39306 AN XY: 74302

African (AFR) AF: 0.463 AC: 19199 AN: 41452

American (AMR) AF: 0.520 AC: 7942 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.686 AC: 2377 AN: 3464

East Asian (EAS) AF: 0.334 AC: 1723 AN: 5162

South Asian (SAS) AF: 0.564 AC: 2719 AN: 4820

European-Finnish (FIN) AF: 0.520 AC: 5496 AN: 10560

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.581 AC: 39514 AN: 67976

Other (OTH) AF: 0.563 AC: 1187 AN: 2110

Alfa AF: 0.559 Hom.: 75760

Bravo AF: 0.522

Asia WGS AF: 0.451 AC: 1573 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.1
DANN	Benign	0.63
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs10931041; hg19: chr2-183685562;