2-203705369-C-T

Variant names:

• chr2-203705369-C-T
• rs3181096

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 0.345 in 151,896 control chromosomes in the GnomAD database, including 9,222 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 0.35 (9222 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 37 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.587 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52426 AN: 151776 Hom.: 9223 Cov.: 31

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.345 AC: 52433 AN: 151896 Hom.: 9222 Cov.: 31 AF XY: 0.346 AC XY: 25696 AN XY: 74238

African (AFR) AF: 0.324 AC: 13403 AN: 41396

American (AMR) AF: 0.324 AC: 4953 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1333 AN: 3470

East Asian (EAS) AF: 0.279 AC: 1443 AN: 5176

South Asian (SAS) AF: 0.605 AC: 2905 AN: 4802

European-Finnish (FIN) AF: 0.336 AC: 3535 AN: 10524

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.351 AC: 23823 AN: 67942

Other (OTH) AF: 0.338 AC: 714 AN: 2112

Alfa AF: 0.357 Hom.: 31380

Bravo AF: 0.338

Asia WGS AF: 0.450 AC: 1567 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	12
DANN	Benign	0.83
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs3181096; hg19: chr2-204570092;