rs10495874

Variant names:

• chr2-37809274-T-C
• rs10495874

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 0.127 in 152,268 control chromosomes in the GnomAD database, including 1,368 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 0.13 (1368 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.08

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.181 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: 0.127 AC: 19365 AN: 152150 Hom.: 1370 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.0462

Gnomad AMR AF: 0.0982

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.00770

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.127 AC: 19375 AN: 152268 Hom.: 1368 Cov.: 32 AF XY: 0.127 AC XY: 9421 AN XY: 74460

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.0982

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.00772

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.151

Gnomad4 OTH AF: 0.133

Alfa AF: 0.147 Hom.: 767

Bravo AF: 0.122

Asia WGS AF: 0.0850 AC: 295 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	15
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10495874; hg19: chr2-38036417;