rs1463592

chr12-55863508-C-A

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 0.251 in 152,062 control chromosomes in the GnomAD database, including 5,101 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 0.25 (5101 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.335 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: 0.250 AC: 38061 AN: 151944 Hom.: 5089 Cov.: 31

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.199

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.251 AC: 38124 AN: 152062 Hom.: 5101 Cov.: 31 AF XY: 0.250 AC XY: 18594 AN XY: 74344

Gnomad4 AFR AF: 0.339

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.201

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.237

Gnomad4 NFE AF: 0.215

Gnomad4 OTH AF: 0.227

Alfa AF: 0.218 Hom.: 2376

Bravo AF: 0.262

Asia WGS AF: 0.206 AC: 716 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.38
Dann	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1463592; hg19: chr12-56257292;