rs1463592

Variant names:

• chr12-55863508-C-A
• rs1463592

Your query was ambiguous. Multiple possible variants found:

• chr12-55863508-C-A
• chr12-55863508-C-G
• chr12-55863508-C-T

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 0.251 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.339 AC: 14078 AN: 41468

American (AMR) AF: 0.264 AC: 4026 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 398 AN: 3468

East Asian (EAS) AF: 0.201 AC: 1037 AN: 5168

South Asian (SAS) AF: 0.161 AC: 776 AN: 4820

European-Finnish (FIN) AF: 0.237 AC: 2506 AN: 10572

Middle Eastern (MID) AF: 0.110 AC: 32 AN: 292

European-Non Finnish (NFE) AF: 0.215 AC: 14610 AN: 67980

Other (OTH) AF: 0.227 AC: 480 AN: 2112

Alfa AF: 0.218 Hom.: 3318

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
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1463592; hg19: chr12-56257292;