chr15-84403620-G-A

Variant names:

• chr15-84403620-G-A
• rs12910334
• ENST00000558731.1:n.2716C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 publications found

Genes affected

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

ENSG00000290690 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000558731.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CSPG4P5	ENST00000558731.1	TSL:6	n.2716C>T		non_coding_transcript_exon	Exon 2 of 3
	ENSG00000290690	ENST00000558801.1	TSL:5	n.6412C>T		non_coding_transcript_exon	Exon 2 of 3

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

African (AFR) AF: 0.0467 AC: 759 AN: 16246

American (AMR) AF: 0.180 AC: 6606 AN: 36788

Ashkenazi Jewish (ASJ) AF: 0.277 AC: 4534 AN: 16356

East Asian (EAS) AF: 0.0804 AC: 2833 AN: 35218

South Asian (SAS) AF: 0.239 AC: 14121 AN: 59086

European-Finnish (FIN) AF: 0.271 AC: 12742 AN: 46972

Middle Eastern (MID) AF: 0.380 AC: 1200 AN: 3162

European-Non Finnish (NFE) AF: 0.287 AC: 91289 AN: 317924

Other (OTH) AF: 0.248 AC: 7385 AN: 29812

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

African (AFR) AF: 0.0477 AC: 1969 AN: 41320

American (AMR) AF: 0.204 AC: 3095 AN: 15170

Ashkenazi Jewish (ASJ) AF: 0.284 AC: 980 AN: 3454

East Asian (EAS) AF: 0.109 AC: 558 AN: 5140

South Asian (SAS) AF: 0.212 AC: 1010 AN: 4756

European-Finnish (FIN) AF: 0.271 AC: 2822 AN: 10402

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.283 AC: 19126 AN: 67596

Other (OTH) AF: 0.216 AC: 453 AN: 2094

Alfa AF: 0.259 Hom.: 2665

Bravo AF: 0.195

Asia WGS AF: 0.162 AC: 564 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	16
DANN	Benign	0.59
PhyloP100		6.5

Splicing

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

Other links and lift over

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