2-203829153-G-T

Variant names:

• chr2-203829153-G-T
• rs231735

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 0.546 in 151,866 control chromosomes in the GnomAD database, including 22,949 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 0.55 (22949 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 54 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.546 AC: 82834 AN: 151746 Hom.: 22916 Cov.: 31

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.550

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.653

Gnomad MID AF: 0.395

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.546 AC: 82923 AN: 151866 Hom.: 22949 Cov.: 31 AF XY: 0.550 AC XY: 40792 AN XY: 74202

African (AFR) AF: 0.561 AC: 23190 AN: 41362

American (AMR) AF: 0.519 AC: 7929 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.462 AC: 1603 AN: 3468

East Asian (EAS) AF: 0.753 AC: 3878 AN: 5152

South Asian (SAS) AF: 0.389 AC: 1872 AN: 4818

European-Finnish (FIN) AF: 0.653 AC: 6889 AN: 10546

Middle Eastern (MID) AF: 0.404 AC: 118 AN: 292

European-Non Finnish (NFE) AF: 0.529 AC: 35902 AN: 67926

Other (OTH) AF: 0.495 AC: 1044 AN: 2110

Alfa AF: 0.529 Hom.: 73807

Bravo AF: 0.542

Asia WGS AF: 0.538 AC: 1868 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.21
DANN	Benign	0.53
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs231735; hg19: chr2-204693876;