2-203835851-G-T

Variant names:

• chr2-203835851-G-T
• rs231790

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 0.517 in 151,956 control chromosomes in the GnomAD database, including 20,701 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 (20701 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.544
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.517 AC: 78483 AN: 151838 Hom.: 20677 Cov.: 31

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.755

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.517 AC: 78568 AN: 151956 Hom.: 20701 Cov.: 31 AF XY: 0.522 AC XY: 38736 AN XY: 74262

African (AFR) AF: 0.462 AC: 19163 AN: 41448

American (AMR) AF: 0.512 AC: 7810 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.440 AC: 1526 AN: 3466

East Asian (EAS) AF: 0.754 AC: 3910 AN: 5186

South Asian (SAS) AF: 0.388 AC: 1864 AN: 4808

European-Finnish (FIN) AF: 0.647 AC: 6807 AN: 10528

Middle Eastern (MID) AF: 0.401 AC: 117 AN: 292

European-Non Finnish (NFE) AF: 0.528 AC: 35871 AN: 67940

Other (OTH) AF: 0.475 AC: 1003 AN: 2112

Alfa AF: 0.523 Hom.: 3945

Bravo AF: 0.510

Asia WGS AF: 0.529 AC: 1838 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.30
DANN	Benign	0.64
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs231790; hg19: chr2-204700574;