2-226241205-C-T

Variant names:

• chr2-226241205-C-T
• rs2943650

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 0.594 in 152,042 control chromosomes in the GnomAD database, including 28,117 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 0.59 (28117 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.206
• Publications: 61 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• 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: 0.594 AC: 90190 AN: 151924 Hom.: 28090 Cov.: 32

Gnomad AFR AF: 0.404

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.710

Gnomad EAS AF: 0.924

Gnomad SAS AF: 0.736

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.594 AC: 90255 AN: 152042 Hom.: 28117 Cov.: 32 AF XY: 0.599 AC XY: 44477 AN XY: 74314

African (AFR) AF: 0.404 AC: 16747 AN: 41466

American (AMR) AF: 0.710 AC: 10843 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.710 AC: 2460 AN: 3466

East Asian (EAS) AF: 0.925 AC: 4765 AN: 5154

South Asian (SAS) AF: 0.737 AC: 3554 AN: 4820

European-Finnish (FIN) AF: 0.627 AC: 6629 AN: 10572

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.637 AC: 43294 AN: 67966

Other (OTH) AF: 0.614 AC: 1297 AN: 2112

Alfa AF: 0.635 Hom.: 19649

Bravo AF: 0.593

Asia WGS AF: 0.818 AC: 2841 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.4
DANN	Benign	0.38
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs2943650; hg19: chr2-227105921;