rs941873

Variant names:

• chr10-79379706-G-A
• rs941873

Your query was ambiguous. Multiple possible variants found:

• chr10-79379706-G-A
• chr10-79379706-G-C

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 0.479 in 151,946 control chromosomes in the GnomAD database, including 17,906 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 0.48 (17906 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.756
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.628 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: 0.479 AC: 72709 AN: 151828 Hom.: 17869 Cov.: 32

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.646

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.479 AC: 72792 AN: 151946 Hom.: 17906 Cov.: 32 AF XY: 0.487 AC XY: 36150 AN XY: 74222

African (AFR) AF: 0.394 AC: 16336 AN: 41446

American (AMR) AF: 0.584 AC: 8926 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.454 AC: 1576 AN: 3470

East Asian (EAS) AF: 0.646 AC: 3330 AN: 5154

South Asian (SAS) AF: 0.488 AC: 2343 AN: 4806

European-Finnish (FIN) AF: 0.588 AC: 6219 AN: 10578

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.478 AC: 32422 AN: 67894

Other (OTH) AF: 0.490 AC: 1032 AN: 2106

Alfa AF: 0.487 Hom.: 45709

Bravo AF: 0.478

Asia WGS AF: 0.559 AC: 1945 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.2
DANN	Benign	0.82
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs941873; hg19: chr10-81139462;