2-233855851-C-T

Variant names:

• chr2-233855851-C-T
• rs887062

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 0.718 in 151,962 control chromosomes in the GnomAD database, including 39,573 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 0.72 (39573 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.293
• Publications: 6 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 (AFR) allele frequency at 95% confidence interval = 0.809 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: 0.718 AC: 109033 AN: 151844 Hom.: 39521 Cov.: 30

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.718

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.727

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.720

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.726

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

GnomAD4 genome AF: 0.718 AC: 109150 AN: 151962 Hom.: 39573 Cov.: 30 AF XY: 0.716 AC XY: 53168 AN XY: 74266

African (AFR) AF: 0.816 AC: 33832 AN: 41454

American (AMR) AF: 0.684 AC: 10447 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.702 AC: 2434 AN: 3468

East Asian (EAS) AF: 0.727 AC: 3735 AN: 5138

South Asian (SAS) AF: 0.544 AC: 2612 AN: 4804

European-Finnish (FIN) AF: 0.720 AC: 7605 AN: 10562

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.678 AC: 46068 AN: 67952

Other (OTH) AF: 0.728 AC: 1536 AN: 2110

Alfa AF: 0.700 Hom.: 50003

Bravo AF: 0.724

Asia WGS AF: 0.623 AC: 2170 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	0.65
DANN	Benign	0.61
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs887062; hg19: chr2-234764497;