rs12633370

chr3-144566733-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 0.0887 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;