rs10497231

Variant names:

• chr2-163128427-G-A
• rs10497231

Your query was ambiguous. Multiple possible variants found:

• chr2-163128427-G-A
• chr2-163128427-G-T

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 0.196 in 150,888 control chromosomes in the GnomAD database, including 3,062 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 0.20 (3062 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.233 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: 0.196 AC: 29553 AN: 150772 Hom.: 3060 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.196 AC: 29550 AN: 150888 Hom.: 3062 Cov.: 32 AF XY: 0.197 AC XY: 14491 AN XY: 73574

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.181

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.233

Gnomad4 NFE AF: 0.236

Gnomad4 OTH AF: 0.205

Alfa AF: 0.213 Hom.: 425

Bravo AF: 0.194

Asia WGS AF: 0.134 AC: 457 AN: 3428

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.20
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10497231; hg19: chr2-163984937;