rs1533140

Variant names:

• chr3-23997889-G-A
• rs1533140

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 0.594 in 152,000 control chromosomes in the GnomAD database, including 27,650 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 0.59 (27650 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.331

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.68 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: 0.594 AC: 90220 AN: 151882 Hom.: 27624 Cov.: 32

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.484

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.597

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.720

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.621

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

GnomAD4 genome AF: 0.594 AC: 90293 AN: 152000 Hom.: 27650 Cov.: 32 AF XY: 0.591 AC XY: 43894 AN XY: 74308

Gnomad4 AFR AF: 0.448

Gnomad4 AMR AF: 0.626

Gnomad4 ASJ AF: 0.687

Gnomad4 EAS AF: 0.418

Gnomad4 SAS AF: 0.598

Gnomad4 FIN AF: 0.591

Gnomad4 NFE AF: 0.685

Gnomad4 OTH AF: 0.619

Alfa AF: 0.659 Hom.: 15123

Bravo AF: 0.589

Asia WGS AF: 0.517 AC: 1801 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1533140; hg19: chr3-24039380;