15-56052433-C-G

Variant names:

• chr15-56052433-C-G
• rs10518832

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 0.305 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.239 AC: 9928 AN: 41464

American (AMR) AF: 0.280 AC: 4274 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.365 AC: 1265 AN: 3464

East Asian (EAS) AF: 0.0327 AC: 169 AN: 5168

South Asian (SAS) AF: 0.291 AC: 1405 AN: 4822

European-Finnish (FIN) AF: 0.369 AC: 3898 AN: 10554

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.361 AC: 24496 AN: 67946

Other (OTH) AF: 0.293 AC: 619 AN: 2110

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
PhyloP100		1.7

Splicing

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

Other links and lift over

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