rs10497760

Variant names:

• chr2-195444739-C-T
• rs10497760

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 0.112 in 152,090 control chromosomes in the GnomAD database, including 1,176 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 0.11 (1176 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0250
• Publications: 4 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 = 0.216 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: 0.112 AC: 17070 AN: 151972 Hom.: 1176 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.0715

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0685

Gnomad OTH AF: 0.0939

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

GnomAD4 genome AF: 0.112 AC: 17100 AN: 152090 Hom.: 1176 Cov.: 32 AF XY: 0.118 AC XY: 8752 AN XY: 74348

African (AFR) AF: 0.141 AC: 5860 AN: 41490

American (AMR) AF: 0.170 AC: 2591 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0715 AC: 248 AN: 3470

East Asian (EAS) AF: 0.226 AC: 1173 AN: 5182

South Asian (SAS) AF: 0.166 AC: 796 AN: 4804

European-Finnish (FIN) AF: 0.147 AC: 1546 AN: 10552

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0685 AC: 4659 AN: 68018

Other (OTH) AF: 0.0967 AC: 204 AN: 2110

Alfa AF: 0.0839 Hom.: 1235

Bravo AF: 0.118

Asia WGS AF: 0.195 AC: 679 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	14
DANN	Benign	0.51
PhyloP100		-0.025

Splicing

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

Other links and lift over

dbSNP: rs10497760; hg19: chr2-196309463;