rs180940

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;