rs13032261

Variant names:

• chr2-226403875-C-A
• rs13032261

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 0.578 in 152,008 control chromosomes in the GnomAD database, including 26,071 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 0.58 (26071 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.189
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.619 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: 0.578 AC: 87864 AN: 151888 Hom.: 26052 Cov.: 33

Gnomad AFR AF: 0.550

Gnomad AMI AF: 0.679

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.613

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.578 AC: 87923 AN: 152008 Hom.: 26071 Cov.: 33 AF XY: 0.579 AC XY: 43002 AN XY: 74306

African (AFR) AF: 0.550 AC: 22785 AN: 41436

American (AMR) AF: 0.499 AC: 7626 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.613 AC: 2125 AN: 3468

East Asian (EAS) AF: 0.183 AC: 944 AN: 5166

South Asian (SAS) AF: 0.614 AC: 2955 AN: 4816

European-Finnish (FIN) AF: 0.671 AC: 7089 AN: 10572

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.624 AC: 42413 AN: 67958

Other (OTH) AF: 0.568 AC: 1201 AN: 2116

Alfa AF: 0.609 Hom.: 16162

Bravo AF: 0.561

Asia WGS AF: 0.407 AC: 1423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.82
DANN	Benign	0.23
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs13032261; hg19: chr2-227268591; COSMIC: COSV53927434;