rs1533140

chr3-23997889-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 0.594 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/exons	MANE	UniProt

Ensembl

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