2-203835851-G-T

Variant names:

• chr2-203835851-G-T
• rs231790

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.462

Gnomad4 AMR AF: 0.512

Gnomad4 ASJ AF: 0.440

Gnomad4 EAS AF: 0.754

Gnomad4 SAS AF: 0.388

Gnomad4 FIN AF: 0.647

Gnomad4 NFE AF: 0.528

Gnomad4 OTH AF: 0.475

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs231790; hg19: chr2-204700574;