2-157350823-G-T

Variant names:

• chr2-157350823-G-T
• rs10497181

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0178 in 152,294 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: 0.416
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0808 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0179 AC: 2718 AN: 152176 Hom.: 92 Cov.: 32

Gnomad AFR AF: 0.00362

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.0849

Gnomad ASJ AF: 0.00605

Gnomad EAS AF: 0.0617

Gnomad SAS AF: 0.0398

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: 2715 AN: 152294 Hom.: 91 Cov.: 32 AF XY: 0.0202 AC XY: 1502 AN XY: 74464

African (AFR) AF: 0.00361 AC: 150 AN: 41568

American (AMR) AF: 0.0846 AC: 1293 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.00605 AC: 21 AN: 3470

East Asian (EAS) AF: 0.0618 AC: 321 AN: 5192

South Asian (SAS) AF: 0.0400 AC: 193 AN: 4822

European-Finnish (FIN) AF: 0.0107 AC: 114 AN: 10612

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.00744 AC: 506 AN: 68022

Other (OTH) AF: 0.0180 AC: 38 AN: 2116

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.0
DANN	Benign	0.67
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs10497181; hg19: chr2-158207335;