2-226243730-C-T

Variant names:

• chr2-226243730-C-T
• rs2943652

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.616

Gnomad4 AMR AF: 0.729

Gnomad4 ASJ AF: 0.709

Gnomad4 EAS AF: 0.925

Gnomad4 SAS AF: 0.737

Gnomad4 FIN AF: 0.628

Gnomad4 NFE AF: 0.637

Gnomad4 OTH AF: 0.657

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2943652; hg19: chr2-227108446;