rs10490649

Variant names:

• chr2-41686408-C-T
• rs10490649

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 0.182 in 151,858 control chromosomes in the GnomAD database, including 2,815 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 0.18 (2815 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.137
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.225 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: 0.182 AC: 27677 AN: 151740 Hom.: 2813 Cov.: 32

Gnomad AFR AF: 0.0883

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.182 AC: 27698 AN: 151858 Hom.: 2815 Cov.: 32 AF XY: 0.183 AC XY: 13592 AN XY: 74202

African (AFR) AF: 0.0882 AC: 3651 AN: 41398

American (AMR) AF: 0.231 AC: 3530 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 645 AN: 3472

East Asian (EAS) AF: 0.224 AC: 1156 AN: 5158

South Asian (SAS) AF: 0.202 AC: 970 AN: 4810

European-Finnish (FIN) AF: 0.207 AC: 2171 AN: 10510

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.220 AC: 14927 AN: 67950

Other (OTH) AF: 0.183 AC: 386 AN: 2104

Alfa AF: 0.200 Hom.: 429

Bravo AF: 0.180

Asia WGS AF: 0.251 AC: 870 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	6.3
DANN	Benign	0.80
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs10490649; hg19: chr2-41913548;