15-53273430-T-G

Variant names:

• chr15-53273430-T-G
• rs12591795

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0233 AC: 967 AN: 41580

American (AMR) AF: 0.0490 AC: 749 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0297 AC: 103 AN: 3470

East Asian (EAS) AF: 0.130 AC: 674 AN: 5174

South Asian (SAS) AF: 0.0845 AC: 408 AN: 4828

European-Finnish (FIN) AF: 0.0472 AC: 502 AN: 10628

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0409 AC: 2781 AN: 67998

Other (OTH) AF: 0.0431 AC: 91 AN: 2112

Alfa AF: 0.0378 Hom.: 195

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
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs12591795; hg19: chr15-53565627;