chr2-52476452-G-A

Variant names:

• chr2-52476452-G-A
• rs12619788

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 0.455 in 151,854 control chromosomes in the GnomAD database, including 16,029 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 0.46 (16029 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.543
• Publications: 6 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 (EAS) allele frequency at 95% confidence interval = 0.517 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: 0.455 AC: 69082 AN: 151736 Hom.: 16022 Cov.: 31

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.455 AC: 69121 AN: 151854 Hom.: 16029 Cov.: 31 AF XY: 0.453 AC XY: 33643 AN XY: 74216

African (AFR) AF: 0.383 AC: 15847 AN: 41390

American (AMR) AF: 0.377 AC: 5754 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1363 AN: 3472

East Asian (EAS) AF: 0.533 AC: 2742 AN: 5140

South Asian (SAS) AF: 0.473 AC: 2280 AN: 4816

European-Finnish (FIN) AF: 0.532 AC: 5601 AN: 10532

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.500 AC: 33951 AN: 67940

Other (OTH) AF: 0.452 AC: 952 AN: 2106

Alfa AF: 0.477 Hom.: 67429

Bravo AF: 0.437

Asia WGS AF: 0.487 AC: 1690 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	10
DANN	Benign	0.77
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs12619788; hg19: chr2-52703590;