chr2-179352004-C-A

Variant names:

• chr2-179352004-C-A
• rs13403289

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 0.483 in 152,014 control chromosomes in the GnomAD database, including 19,636 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 0.48 (19636 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 4 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 (SAS) allele frequency at 95% confidence interval = 0.583 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: 0.483 AC: 73318 AN: 151894 Hom.: 19602 Cov.: 31

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.725

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.630

Gnomad EAS AF: 0.569

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.483 AC: 73393 AN: 152014 Hom.: 19636 Cov.: 31 AF XY: 0.492 AC XY: 36538 AN XY: 74314

African (AFR) AF: 0.236 AC: 9770 AN: 41480

American (AMR) AF: 0.538 AC: 8208 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.630 AC: 2184 AN: 3468

East Asian (EAS) AF: 0.570 AC: 2939 AN: 5158

South Asian (SAS) AF: 0.601 AC: 2899 AN: 4824

European-Finnish (FIN) AF: 0.657 AC: 6936 AN: 10564

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.567 AC: 38533 AN: 67940

Other (OTH) AF: 0.514 AC: 1087 AN: 2116

Alfa AF: 0.539 Hom.: 65622

Bravo AF: 0.462

Asia WGS AF: 0.564 AC: 1961 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.40
DANN	Benign	0.39
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs13403289; hg19: chr2-180216731;