rs12910334

chr15-84403620-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000558731.1(CSPG4P5):n.2716C>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.241 in 712,682 control chromosomes in the GnomAD database, including 23,738 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 0.20 (4016 hom., cov: 28)
  • Exomes 𝑓: 0.25 (19722 hom.)
• Consequence: CSPG4P5 ENST00000558731.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.54

Genes affected

CSPG4P5 (HGNC:29403): (chondroitin sulfate proteoglycan 4 pseudogene 5)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.28 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSPG4P5	ENST00000558731.1	n.2716C>T		non_coding_transcript_exon_variant	2/3
	ENST00000558801.1	n.6412C>T		non_coding_transcript_exon_variant	2/3	5

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30587 AN: 151000 Hom.: 4016 Cov.: 28

Gnomad AFR AF: 0.0477

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.219

GnomAD4 exome AF: 0.252 AC: 141469 AN: 561564 Hom.: 19722 Cov.: 0 AF XY: 0.255 AC XY: 77851 AN XY: 304764

Gnomad4 AFR exome AF: 0.0467

Gnomad4 AMR exome AF: 0.180

Gnomad4 ASJ exome AF: 0.277

Gnomad4 EAS exome AF: 0.0804

Gnomad4 SAS exome AF: 0.239

Gnomad4 FIN exome AF: 0.271

Gnomad4 NFE exome AF: 0.287

Gnomad4 OTH exome AF: 0.248

GnomAD4 genome AF: 0.202 AC: 30581 AN: 151118 Hom.: 4016 Cov.: 28 AF XY: 0.201 AC XY: 14806 AN XY: 73756

Gnomad4 AFR AF: 0.0477

Gnomad4 AMR AF: 0.204

Gnomad4 ASJ AF: 0.284

Gnomad4 EAS AF: 0.109

Gnomad4 SAS AF: 0.212

Gnomad4 FIN AF: 0.271

Gnomad4 NFE AF: 0.283

Gnomad4 OTH AF: 0.216

Alfa AF: 0.260 Hom.: 2369

Bravo AF: 0.195

Asia WGS AF: 0.162 AC: 564 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
Cadd	Benign	16
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12910334; hg19: chr15-84958318; COSMIC: COSV71786703;