2-231931900-T-C

Variant names:

• chr2-231931900-T-C
• rs749052

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 0.0732 in 152,212 control chromosomes in the GnomAD database, including 519 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 0.073 (519 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.790
• Publications: 23 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.105 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: 0.0732 AC: 11128 AN: 152094 Hom.: 518 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.0481

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.00404

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.0251

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.0633

Gnomad OTH AF: 0.0792

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

GnomAD4 genome AF: 0.0732 AC: 11139 AN: 152212 Hom.: 519 Cov.: 32 AF XY: 0.0715 AC XY: 5322 AN XY: 74414

African (AFR) AF: 0.108 AC: 4465 AN: 41510

American (AMR) AF: 0.0480 AC: 734 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 487 AN: 3472

East Asian (EAS) AF: 0.00386 AC: 20 AN: 5188

South Asian (SAS) AF: 0.107 AC: 518 AN: 4822

European-Finnish (FIN) AF: 0.0251 AC: 266 AN: 10602

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.0633 AC: 4303 AN: 68016

Other (OTH) AF: 0.0779 AC: 164 AN: 2106

Alfa AF: 0.0679 Hom.: 1684

Bravo AF: 0.0755

Asia WGS AF: 0.0460 AC: 160 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.89
DANN	Benign	0.75
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs749052; hg19: chr2-232796610;