rs13412582

Variant names:

• chr2-226469312-C-A
• rs13412582

Your query was ambiguous. Multiple possible variants found:

• chr2-226469312-C-A
• chr2-226469312-C-G
• chr2-226469312-C-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 0.505 in 150,968 control chromosomes in the GnomAD database, including 20,267 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 0.50 (20267 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.574
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.89 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: 0.505 AC: 76182 AN: 150850 Hom.: 20256 Cov.: 27

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.649

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.912

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.565

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

GnomAD4 genome AF: 0.505 AC: 76212 AN: 150968 Hom.: 20267 Cov.: 27 AF XY: 0.508 AC XY: 37475 AN XY: 73756

African (AFR) AF: 0.367 AC: 15086 AN: 41092

American (AMR) AF: 0.586 AC: 8901 AN: 15178

Ashkenazi Jewish (ASJ) AF: 0.663 AC: 2296 AN: 3462

East Asian (EAS) AF: 0.912 AC: 4659 AN: 5108

South Asian (SAS) AF: 0.600 AC: 2866 AN: 4780

European-Finnish (FIN) AF: 0.478 AC: 4948 AN: 10348

Middle Eastern (MID) AF: 0.684 AC: 197 AN: 288

European-Non Finnish (NFE) AF: 0.524 AC: 35470 AN: 67700

Other (OTH) AF: 0.570 AC: 1201 AN: 2106

Alfa AF: 0.504 Hom.: 2423

Bravo AF: 0.510

Asia WGS AF: 0.707 AC: 2458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.6
DANN	Benign	0.70
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs13412582; hg19: chr2-227334028;