2-203876143-C-T

Variant names:

• chr2-203876143-C-T
• rs231726

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 0.362 in 151,938 control chromosomes in the GnomAD database, including 10,394 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 0.36 (10394 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65
• Publications: 41 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.573 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: 0.362 AC: 55001 AN: 151820 Hom.: 10386 Cov.: 32

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.362 AC: 55052 AN: 151938 Hom.: 10394 Cov.: 32 AF XY: 0.369 AC XY: 27403 AN XY: 74266

African (AFR) AF: 0.366 AC: 15146 AN: 41410

American (AMR) AF: 0.385 AC: 5889 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 886 AN: 3470

East Asian (EAS) AF: 0.590 AC: 3040 AN: 5152

South Asian (SAS) AF: 0.279 AC: 1347 AN: 4824

European-Finnish (FIN) AF: 0.485 AC: 5116 AN: 10558

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.332 AC: 22554 AN: 67932

Other (OTH) AF: 0.316 AC: 665 AN: 2106

Alfa AF: 0.333 Hom.: 38599

Bravo AF: 0.359

Asia WGS AF: 0.389 AC: 1349 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.23
DANN	Benign	0.38
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs231726; hg19: chr2-204740866;