2-226234464-C-T

Variant names:

• chr2-226234464-C-T
• rs2943645

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 0.66 in 152,034 control chromosomes in the GnomAD database, including 33,345 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 0.66 (33345 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.971
• Publications: 62 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

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.660 AC: 100226 AN: 151916 Hom.: 33312 Cov.: 32

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.712

Gnomad EAS AF: 0.926

Gnomad SAS AF: 0.760

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.652

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

GnomAD4 genome AF: 0.660 AC: 100306 AN: 152034 Hom.: 33345 Cov.: 32 AF XY: 0.662 AC XY: 49171 AN XY: 74310

African (AFR) AF: 0.631 AC: 26155 AN: 41458

American (AMR) AF: 0.733 AC: 11188 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.712 AC: 2470 AN: 3470

East Asian (EAS) AF: 0.927 AC: 4791 AN: 5168

South Asian (SAS) AF: 0.761 AC: 3665 AN: 4814

European-Finnish (FIN) AF: 0.627 AC: 6630 AN: 10574

Middle Eastern (MID) AF: 0.531 AC: 155 AN: 292

European-Non Finnish (NFE) AF: 0.638 AC: 43353 AN: 67972

Other (OTH) AF: 0.655 AC: 1380 AN: 2106

Alfa AF: 0.650 Hom.: 97958

Bravo AF: 0.668

Asia WGS AF: 0.842 AC: 2928 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.63
DANN	Benign	0.29
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs2943645; hg19: chr2-227099180;