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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.394

Gnomad4 AMR AF: 0.584

Gnomad4 ASJ AF: 0.454

Gnomad4 EAS AF: 0.646

Gnomad4 SAS AF: 0.488

Gnomad4 FIN AF: 0.588

Gnomad4 NFE AF: 0.478

Gnomad4 OTH AF: 0.490

Alfa AF: 0.486 Hom.: 16570

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs941873; hg19: chr10-81139462;