rs10495874

Positions:

• chr2-37809274-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;