rs10497182

Variant names:

• chr2-157355517-T-A
• rs10497182

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 0.0178 in 152,304 control chromosomes in the GnomAD database, including 91 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 0.018 (91 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.33

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0807 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: 0.0178 AC: 2714 AN: 152186 Hom.: 92 Cov.: 32

Gnomad AFR AF: 0.00359

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.0848

Gnomad ASJ AF: 0.00605

Gnomad EAS AF: 0.0618

Gnomad SAS AF: 0.0395

Gnomad FIN AF: 0.0107

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00744

Gnomad OTH AF: 0.0186

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

GnomAD4 genome AF: 0.0178 AC: 2711 AN: 152304 Hom.: 91 Cov.: 32 AF XY: 0.0202 AC XY: 1502 AN XY: 74488

Gnomad4 AFR AF: 0.00358

Gnomad4 AMR AF: 0.0845

Gnomad4 ASJ AF: 0.00605

Gnomad4 EAS AF: 0.0619

Gnomad4 SAS AF: 0.0398

Gnomad4 FIN AF: 0.0107

Gnomad4 NFE AF: 0.00744

Gnomad4 OTH AF: 0.0180

Alfa AF: 0.0104 Hom.: 7

Bravo AF: 0.0224

Asia WGS AF: 0.0480 AC: 169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	16
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10497182; hg19: chr2-158212029;