rs12910334
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
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
ENST00000558731.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 6.54
Genes affected
CSPG4P5 (HGNC:29403): (chondroitin sulfate proteoglycan 4 pseudogene 5)
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ACMG classification
Classification made for transcript
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: 30587AN: 151000Hom.: 4016 Cov.: 28
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GnomAD4 exome AF: 0.252 AC: 141469AN: 561564Hom.: 19722 Cov.: 0 AF XY: 0.255 AC XY: 77851AN XY: 304764
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GnomAD4 genome ? AF: 0.202 AC: 30581AN: 151118Hom.: 4016 Cov.: 28 AF XY: 0.201 AC XY: 14806AN XY: 73756
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at