rs1433452

chr15-87051893-C-T

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 0.463 in 152,008 control chromosomes in the GnomAD database, including 18,838 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 0.46 (18838 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0440

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.733 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: 0.462 AC: 70191 AN: 151890 Hom.: 18781 Cov.: 32

Gnomad AFR AF: 0.739

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.442

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

GnomAD4 genome AF: 0.463 AC: 70310 AN: 152008 Hom.: 18838 Cov.: 32 AF XY: 0.462 AC XY: 34339 AN XY: 74310

Gnomad4 AFR AF: 0.740

Gnomad4 AMR AF: 0.457

Gnomad4 ASJ AF: 0.389

Gnomad4 EAS AF: 0.508

Gnomad4 SAS AF: 0.282

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.322

Gnomad4 OTH AF: 0.445

Alfa AF: 0.411 Hom.: 1828

Bravo AF: 0.481

Asia WGS AF: 0.420 AC: 1464 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.98
Dann	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1433452; hg19: chr15-87595124;