rs10497795

Variant names:

• chr2-196622901-C-A
• rs10497795

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 0.102 in 152,220 control chromosomes in the GnomAD database, including 842 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 0.10 (842 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.126 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: 0.102 AC: 15572 AN: 152102 Hom.: 841 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.0834

Gnomad ASJ AF: 0.0733

Gnomad EAS AF: 0.00694

Gnomad SAS AF: 0.0344

Gnomad FIN AF: 0.0690

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.102 AC: 15583 AN: 152220 Hom.: 842 Cov.: 32 AF XY: 0.0995 AC XY: 7408 AN XY: 74426

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.0832

Gnomad4 ASJ AF: 0.0733

Gnomad4 EAS AF: 0.00676

Gnomad4 SAS AF: 0.0338

Gnomad4 FIN AF: 0.0690

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.106

Alfa AF: 0.101 Hom.: 121

Bravo AF: 0.105

Asia WGS AF: 0.0270 AC: 94 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10497795; hg19: chr2-197487625;