chr3-144566733-G-A

Variant names:

• chr3-144566733-G-A
• rs12633370

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 0.0887 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0755 AC: 3119 AN: 41292

American (AMR) AF: 0.0961 AC: 1464 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 458 AN: 3470

East Asian (EAS) AF: 0.265 AC: 1364 AN: 5146

South Asian (SAS) AF: 0.160 AC: 771 AN: 4808

European-Finnish (FIN) AF: 0.0472 AC: 496 AN: 10518

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0803 AC: 5455 AN: 67930

Other (OTH) AF: 0.101 AC: 212 AN: 2108

Alfa AF: 0.0880 Hom.: 107

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
PhyloP100		-3.3

Splicing

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

Other links and lift over

dbSNP: rs12633370; hg19: chr3-144285575;