rs2679184

Variant names:

• chr2-231914513-T-C
• rs2679184

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 0.325 in 151,646 control chromosomes in the GnomAD database, including 9,049 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 0.32 (9049 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.615
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.51 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: 0.325 AC: 49200 AN: 151526 Hom.: 9027 Cov.: 30

Gnomad AFR AF: 0.516

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.325 AC: 49272 AN: 151646 Hom.: 9049 Cov.: 30 AF XY: 0.322 AC XY: 23852 AN XY: 74088

African (AFR) AF: 0.516 AC: 21325 AN: 41306

American (AMR) AF: 0.288 AC: 4400 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 936 AN: 3466

East Asian (EAS) AF: 0.189 AC: 969 AN: 5132

South Asian (SAS) AF: 0.234 AC: 1126 AN: 4804

European-Finnish (FIN) AF: 0.256 AC: 2685 AN: 10496

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.249 AC: 16884 AN: 67880

Other (OTH) AF: 0.313 AC: 658 AN: 2102

Alfa AF: 0.270 Hom.: 9859

Bravo AF: 0.336

Asia WGS AF: 0.193 AC: 673 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	4.8
DANN	Benign	0.75
PhyloP100		0.61

Splicing

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

Other links and lift over

dbSNP: rs2679184; hg19: chr2-232779223;