2-226243730-C-T

Variant names:

• chr2-226243730-C-T
• rs2943652

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 0.654 in 151,860 control chromosomes in the GnomAD database, including 32,807 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 0.65 (32807 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.521
• Publications: 30 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.903 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: 0.654 AC: 99280 AN: 151742 Hom.: 32776 Cov.: 32

Gnomad AFR AF: 0.617

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.729

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.925

Gnomad SAS AF: 0.736

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.654

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

GnomAD4 genome AF: 0.654 AC: 99358 AN: 151860 Hom.: 32807 Cov.: 32 AF XY: 0.656 AC XY: 48705 AN XY: 74218

African (AFR) AF: 0.616 AC: 25542 AN: 41434

American (AMR) AF: 0.729 AC: 11136 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.709 AC: 2462 AN: 3472

East Asian (EAS) AF: 0.925 AC: 4789 AN: 5176

South Asian (SAS) AF: 0.737 AC: 3556 AN: 4822

European-Finnish (FIN) AF: 0.628 AC: 6579 AN: 10476

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.637 AC: 43239 AN: 67904

Other (OTH) AF: 0.657 AC: 1386 AN: 2108

Alfa AF: 0.642 Hom.: 4685

Bravo AF: 0.662

Asia WGS AF: 0.825 AC: 2842 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.23
DANN	Benign	0.50
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs2943652; hg19: chr2-227108446;