rs2497401

Variant names:

• chr13-85277744-G-A
• rs2497401

Your query was ambiguous. Multiple possible variants found:

• chr13-85277744-G-A
• chr13-85277744-G-C
• chr13-85277744-G-T

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 0.125 in 152,102 control chromosomes in the GnomAD database, including 1,296 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 0.12 (1296 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.393
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.134 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: 0.125 AC: 18987 AN: 151984 Hom.: 1292 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.0891

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.0279

Gnomad SAS AF: 0.0902

Gnomad FIN AF: 0.0926

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.125 AC: 19009 AN: 152102 Hom.: 1296 Cov.: 32 AF XY: 0.121 AC XY: 9021 AN XY: 74376

African (AFR) AF: 0.131 AC: 5455 AN: 41514

American (AMR) AF: 0.0888 AC: 1357 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 784 AN: 3468

East Asian (EAS) AF: 0.0280 AC: 145 AN: 5186

South Asian (SAS) AF: 0.0901 AC: 435 AN: 4830

European-Finnish (FIN) AF: 0.0926 AC: 980 AN: 10586

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9254 AN: 67928

Other (OTH) AF: 0.142 AC: 299 AN: 2108

Alfa AF: 0.130 Hom.: 2188

Bravo AF: 0.123

Asia WGS AF: 0.0660 AC: 229 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.9
DANN	Benign	0.48
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs2497401; hg19: chr13-85851879;