2-203849168-G-T

Variant names:

• chr2-203849168-G-T
• rs231811

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 0.578 in 151,964 control chromosomes in the GnomAD database, including 25,728 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 0.58 (25728 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.148
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.732 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: 0.578 AC: 87773 AN: 151846 Hom.: 25695 Cov.: 32

Gnomad AFR AF: 0.553

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.578 AC: 87864 AN: 151964 Hom.: 25728 Cov.: 32 AF XY: 0.582 AC XY: 43233 AN XY: 74278

African (AFR) AF: 0.554 AC: 22941 AN: 41428

American (AMR) AF: 0.570 AC: 8700 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 1683 AN: 3466

East Asian (EAS) AF: 0.752 AC: 3886 AN: 5168

South Asian (SAS) AF: 0.400 AC: 1926 AN: 4812

European-Finnish (FIN) AF: 0.693 AC: 7309 AN: 10554

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.583 AC: 39620 AN: 67950

Other (OTH) AF: 0.535 AC: 1130 AN: 2114

Alfa AF: 0.539 Hom.: 6524

Bravo AF: 0.573

Asia WGS AF: 0.537 AC: 1866 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.79
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs231811; hg19: chr2-204713891;