chr2-226229029-T-C

Variant names:

• chr2-226229029-T-C
• rs2943641

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 0.679 in 151,948 control chromosomes in the GnomAD database, including 35,250 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 0.68 (35250 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.150
• Publications: 227 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.678 AC: 103008 AN: 151830 Hom.: 35212 Cov.: 31

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.926

Gnomad SAS AF: 0.761

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.669

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

GnomAD4 genome AF: 0.679 AC: 103099 AN: 151948 Hom.: 35250 Cov.: 31 AF XY: 0.680 AC XY: 50464 AN XY: 74260

African (AFR) AF: 0.693 AC: 28717 AN: 41442

American (AMR) AF: 0.741 AC: 11314 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.717 AC: 2485 AN: 3466

East Asian (EAS) AF: 0.927 AC: 4774 AN: 5152

South Asian (SAS) AF: 0.762 AC: 3674 AN: 4824

European-Finnish (FIN) AF: 0.627 AC: 6620 AN: 10566

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.639 AC: 43420 AN: 67916

Other (OTH) AF: 0.673 AC: 1418 AN: 2108

Alfa AF: 0.659 Hom.: 147168

Bravo AF: 0.689

Asia WGS AF: 0.847 AC: 2942 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.6
DANN	Benign	0.88
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs2943641; hg19: chr2-227093745;