rs12619788

Variant names:

• chr2-52476452-G-A
• rs12619788

Your query was ambiguous. Multiple possible variants found:

• chr2-52476452-G-A
• chr2-52476452-G-C
• chr2-52476452-G-T

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 0.455 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

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 (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

Gnomad4 AFR AF: 0.383

Gnomad4 AMR AF: 0.377

Gnomad4 ASJ AF: 0.393

Gnomad4 EAS AF: 0.533

Gnomad4 SAS AF: 0.473

Gnomad4 FIN AF: 0.532

Gnomad4 NFE AF: 0.500

Gnomad4 OTH AF: 0.452

Alfa AF: 0.473 Hom.: 28863

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12619788; hg19: chr2-52703590;