rs180940

Variant names:

• chr10-113962652-A-G
• rs180940

Your query was ambiguous. Multiple possible variants found:

• chr10-113962652-A-G
• chr10-113962652-A-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 0.639 in 151,462 control chromosomes in the GnomAD database, including 31,397 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 0.64 (31397 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.407

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.672 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: 0.639 AC: 96707 AN: 151346 Hom.: 31370 Cov.: 28

Gnomad AFR AF: 0.555

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.795

Gnomad MID AF: 0.583

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.639 AC: 96787 AN: 151462 Hom.: 31397 Cov.: 28 AF XY: 0.646 AC XY: 47818 AN XY: 73984

Gnomad4 AFR AF: 0.555

Gnomad4 AMR AF: 0.650

Gnomad4 ASJ AF: 0.541

Gnomad4 EAS AF: 0.480

Gnomad4 SAS AF: 0.687

Gnomad4 FIN AF: 0.795

Gnomad4 NFE AF: 0.677

Gnomad4 OTH AF: 0.609

Alfa AF: 0.658 Hom.: 9957

Bravo AF: 0.620

Asia WGS AF: 0.559 AC: 1940 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.66
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs180940; hg19: chr10-115722411;