rs2890652

Variant names:

• chr2-142202362-T-C
• rs2890652

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 0.201 in 152,080 control chromosomes in the GnomAD database, including 3,700 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 0.20 (3700 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.58
• Publications: 114 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30567 AN: 151962 Hom.: 3687 Cov.: 32

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.0613

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.201 AC: 30612 AN: 152080 Hom.: 3700 Cov.: 32 AF XY: 0.201 AC XY: 14920 AN XY: 74356

African (AFR) AF: 0.319 AC: 13222 AN: 41468

American (AMR) AF: 0.117 AC: 1796 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 497 AN: 3470

East Asian (EAS) AF: 0.00251 AC: 13 AN: 5186

South Asian (SAS) AF: 0.0607 AC: 293 AN: 4826

European-Finnish (FIN) AF: 0.266 AC: 2807 AN: 10558

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.167 AC: 11370 AN: 67970

Other (OTH) AF: 0.176 AC: 372 AN: 2110

Alfa AF: 0.166 Hom.: 3517

Bravo AF: 0.197

Asia WGS AF: 0.0500 AC: 174 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.34
DANN	Benign	0.30
PhyloP100		-3.6

Splicing

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

Other links and lift over

dbSNP: rs2890652; hg19: chr2-142959931;