rs2679184

Variant names:

• chr2-231914513-T-C
• rs2679184

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.516

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.270

Gnomad4 EAS AF: 0.189

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.256

Gnomad4 NFE AF: 0.249

Gnomad4 OTH AF: 0.313

Alfa AF: 0.262 Hom.: 7209

Bravo AF: 0.336

Asia WGS AF: 0.193 AC: 673 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2679184; hg19: chr2-232779223;