2-203842694-C-T

Variant names:

• chr2-203842694-C-T
• rs231799

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 0.516 in 151,982 control chromosomes in the GnomAD database, including 20,611 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 0.52 (20611 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.65
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.733 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: 0.516 AC: 78296 AN: 151864 Hom.: 20590 Cov.: 32

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.646

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.516 AC: 78372 AN: 151982 Hom.: 20611 Cov.: 32 AF XY: 0.520 AC XY: 38638 AN XY: 74292

African (AFR) AF: 0.459 AC: 19009 AN: 41434

American (AMR) AF: 0.509 AC: 7781 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1528 AN: 3468

East Asian (EAS) AF: 0.752 AC: 3893 AN: 5174

South Asian (SAS) AF: 0.387 AC: 1866 AN: 4816

European-Finnish (FIN) AF: 0.646 AC: 6814 AN: 10556

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.528 AC: 35864 AN: 67944

Other (OTH) AF: 0.475 AC: 1003 AN: 2110

Alfa AF: 0.490 Hom.: 8509

Bravo AF: 0.508

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.070
DANN	Benign	0.46
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs231799; hg19: chr2-204707417;