rs12742463

Positions:

• chr1-158360452-G-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 0.184 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.406

Gnomad4 AMR AF: 0.0881

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0988

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.161

Alfa AF: 0.110 Hom.: 2292

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12742463; hg19: chr1-158330242;