rs12633370

Variant names:

• chr3-144566733-G-A
• rs12633370

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 0.0887 in 151,706 control chromosomes in the GnomAD database, including 738 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 0.089 (738 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.26

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.253 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: 0.0886 AC: 13431 AN: 151586 Hom.: 736 Cov.: 32

Gnomad AFR AF: 0.0753

Gnomad AMI AF: 0.0914

Gnomad AMR AF: 0.0962

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.0472

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0804

Gnomad OTH AF: 0.0997

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

GnomAD4 genome AF: 0.0887 AC: 13450 AN: 151706 Hom.: 738 Cov.: 32 AF XY: 0.0900 AC XY: 6669 AN XY: 74132

Gnomad4 AFR AF: 0.0755

Gnomad4 AMR AF: 0.0961

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.265

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.0472

Gnomad4 NFE AF: 0.0803

Gnomad4 OTH AF: 0.101

Alfa AF: 0.0883 Hom.: 104

Bravo AF: 0.0901

Asia WGS AF: 0.229 AC: 793 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.13
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12633370; hg19: chr3-144285575;