15-56052433-C-G

Variant names:

• chr15-56052433-C-G
• rs10518832

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 0.305 in 152,006 control chromosomes in the GnomAD database, including 7,423 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 0.31 (7423 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.72

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.357 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: 0.305 AC: 46382 AN: 151888 Hom.: 7421 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.0324

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.305 AC: 46411 AN: 152006 Hom.: 7423 Cov.: 32 AF XY: 0.302 AC XY: 22460 AN XY: 74308

Gnomad4 AFR AF: 0.239

Gnomad4 AMR AF: 0.280

Gnomad4 ASJ AF: 0.365

Gnomad4 EAS AF: 0.0327

Gnomad4 SAS AF: 0.291

Gnomad4 FIN AF: 0.369

Gnomad4 NFE AF: 0.361

Gnomad4 OTH AF: 0.293

Alfa AF: 0.196 Hom.: 433

Bravo AF: 0.295

Asia WGS AF: 0.150 AC: 522 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	11
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10518832; hg19: chr15-56344631; COSMIC: COSV53421358;