rs2943640

Variant names:

• chr2-226228869-A-C
• rs2943640

Your query was ambiguous. Multiple possible variants found:

• chr2-226228869-A-C
• chr2-226228869-A-G

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 0.747 in 152,114 control chromosomes in the GnomAD database, including 43,559 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 0.75 (43559 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65
• Publications: 83 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.905 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: 0.747 AC: 113535 AN: 151996 Hom.: 43490 Cov.: 32

Gnomad AFR AF: 0.912

Gnomad AMI AF: 0.668

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.927

Gnomad SAS AF: 0.798

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.646

Gnomad OTH AF: 0.730

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

GnomAD4 genome AF: 0.747 AC: 113666 AN: 152114 Hom.: 43559 Cov.: 32 AF XY: 0.746 AC XY: 55485 AN XY: 74330

African (AFR) AF: 0.912 AC: 37893 AN: 41534

American (AMR) AF: 0.771 AC: 11780 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.724 AC: 2512 AN: 3470

East Asian (EAS) AF: 0.927 AC: 4797 AN: 5174

South Asian (SAS) AF: 0.798 AC: 3846 AN: 4822

European-Finnish (FIN) AF: 0.628 AC: 6619 AN: 10548

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.646 AC: 43883 AN: 67960

Other (OTH) AF: 0.733 AC: 1551 AN: 2116

Alfa AF: 0.685 Hom.: 108023

Bravo AF: 0.766

Asia WGS AF: 0.876 AC: 3043 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.82
DANN	Benign	0.47
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs2943640; hg19: chr2-227093585;