rs1452142

Positions:

• chr3-132894632-A-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 0.386 in 151,810 control chromosomes in the GnomAD database, including 12,118 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 0.39 (12118 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.458 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: 0.386 AC: 58583 AN: 151700 Hom.: 12113 Cov.: 31

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.0603

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.386 AC: 58596 AN: 151810 Hom.: 12118 Cov.: 31 AF XY: 0.386 AC XY: 28647 AN XY: 74184

Gnomad4 AFR AF: 0.271

Gnomad4 AMR AF: 0.443

Gnomad4 ASJ AF: 0.390

Gnomad4 EAS AF: 0.0604

Gnomad4 SAS AF: 0.380

Gnomad4 FIN AF: 0.431

Gnomad4 NFE AF: 0.462

Gnomad4 OTH AF: 0.383

Alfa AF: 0.421 Hom.: 1709

Bravo AF: 0.379

Asia WGS AF: 0.222 AC: 774 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.84
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1452142; hg19: chr3-132613476; COSMIC: COSV60112508;