15-53273430-T-G

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 0.0413 in 152,280 control chromosomes in the GnomAD database, including 179 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 0.041 (179 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.122 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: 0.0414 AC: 6295 AN: 152162 Hom.: 180 Cov.: 33

Gnomad AFR AF: 0.0233

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0492

Gnomad ASJ AF: 0.0297

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.0851

Gnomad FIN AF: 0.0472

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0409

Gnomad OTH AF: 0.0431

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

GnomAD4 genome AF: 0.0413 AC: 6291 AN: 152280 Hom.: 179 Cov.: 33 AF XY: 0.0436 AC XY: 3244 AN XY: 74438

Gnomad4 AFR AF: 0.0233

Gnomad4 AMR AF: 0.0490

Gnomad4 ASJ AF: 0.0297

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.0845

Gnomad4 FIN AF: 0.0472

Gnomad4 NFE AF: 0.0409

Gnomad4 OTH AF: 0.0431

Alfa AF: 0.0361 Hom.: 129

Bravo AF: 0.0407

Asia WGS AF: 0.110 AC: 382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	5.2
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12591795; hg19: chr15-53565627;