rs12595433

Variant names:

• chr15-62998446-G-A
• rs12595433

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 0.369 in 152,072 control chromosomes in the GnomAD database, including 10,674 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 0.37 (10674 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.904

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.544 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: 0.369 AC: 56019 AN: 151954 Hom.: 10649 Cov.: 33

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.369 AC: 56084 AN: 152072 Hom.: 10674 Cov.: 33 AF XY: 0.372 AC XY: 27682 AN XY: 74342

Gnomad4 AFR AF: 0.403

Gnomad4 AMR AF: 0.420

Gnomad4 ASJ AF: 0.362

Gnomad4 EAS AF: 0.561

Gnomad4 SAS AF: 0.521

Gnomad4 FIN AF: 0.305

Gnomad4 NFE AF: 0.323

Gnomad4 OTH AF: 0.376

Alfa AF: 0.344 Hom.: 15564

Bravo AF: 0.377

Asia WGS AF: 0.563 AC: 1960 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.072
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12595433; hg19: chr15-63290645;