rs12742463

Variant names:

• chr1-158360452-G-A
• rs12742463

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 0.184 in 152,112 control chromosomes in the GnomAD database, including 4,001 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 0.18 (4001 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.139
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.401 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: 0.184 AC: 27916 AN: 151994 Hom.: 3986 Cov.: 32

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.0883

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0994

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.184 AC: 27975 AN: 152112 Hom.: 4001 Cov.: 32 AF XY: 0.180 AC XY: 13395 AN XY: 74368

African (AFR) AF: 0.406 AC: 16818 AN: 41422

American (AMR) AF: 0.0881 AC: 1346 AN: 15280

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

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5188

South Asian (SAS) AF: 0.0988 AC: 477 AN: 4826

European-Finnish (FIN) AF: 0.107 AC: 1137 AN: 10600

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7349 AN: 68010

Other (OTH) AF: 0.161 AC: 339 AN: 2112

Alfa AF: 0.130 Hom.: 6098

Bravo AF: 0.190

Asia WGS AF: 0.0660 AC: 230 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	1.2
DANN	Benign	0.55
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs12742463; hg19: chr1-158330242;