rs12593363

Variant names:

• chr15-89241885-A-G
• rs12593363

Your query was ambiguous. Multiple possible variants found:

• chr15-89241885-A-G
• chr15-89241885-A-T

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 0.353 in 151,822 control chromosomes in the GnomAD database, including 9,793 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 0.35 (9793 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.383
• Publications: 12 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 (NFE) allele frequency at 95% confidence interval = 0.39 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: 0.353 AC: 53541 AN: 151704 Hom.: 9788 Cov.: 31

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.353 AC: 53561 AN: 151822 Hom.: 9793 Cov.: 31 AF XY: 0.358 AC XY: 26535 AN XY: 74146

African (AFR) AF: 0.258 AC: 10699 AN: 41396

American (AMR) AF: 0.337 AC: 5144 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.371 AC: 1285 AN: 3468

East Asian (EAS) AF: 0.331 AC: 1706 AN: 5160

South Asian (SAS) AF: 0.391 AC: 1883 AN: 4818

European-Finnish (FIN) AF: 0.468 AC: 4914 AN: 10504

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.394 AC: 26753 AN: 67924

Other (OTH) AF: 0.343 AC: 722 AN: 2102

Alfa AF: 0.373 Hom.: 5973

Bravo AF: 0.343

Asia WGS AF: 0.342 AC: 1187 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	9.6
DANN	Benign	0.85
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs12593363; hg19: chr15-89785116;