rs12619788

Positions:

• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;