rs1433452

Variant names:

• chr15-87051893-C-T
• rs1433452

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;