rs491340

Variant names:

• chr2-238413498-G-A
• rs491340

Your query was ambiguous. Multiple possible variants found:

• chr2-238413498-G-A
• chr2-238413498-G-C

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 0.239 in 152,080 control chromosomes in the GnomAD database, including 5,259 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 0.24 (5259 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.351 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: 0.239 AC: 36350 AN: 151962 Hom.: 5262 Cov.: 33

Gnomad AFR AF: 0.0734

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.239 AC: 36347 AN: 152080 Hom.: 5259 Cov.: 33 AF XY: 0.238 AC XY: 17709 AN XY: 74338

African (AFR) AF: 0.0734 AC: 3047 AN: 41504

American (AMR) AF: 0.359 AC: 5489 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1257 AN: 3472

East Asian (EAS) AF: 0.255 AC: 1317 AN: 5170

South Asian (SAS) AF: 0.223 AC: 1078 AN: 4828

European-Finnish (FIN) AF: 0.249 AC: 2625 AN: 10556

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.304 AC: 20644 AN: 67960

Other (OTH) AF: 0.260 AC: 549 AN: 2108

Alfa AF: 0.277 Hom.: 840

Bravo AF: 0.240

Asia WGS AF: 0.261 AC: 909 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.2
DANN	Benign	0.13
PhyloP100		0.061

Splicing

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

Other links and lift over

dbSNP: rs491340; hg19: chr2-239322139;