7-121099908-GTTTT-G
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_024913.5(CPED1):c.750-6_750-3del variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000401 in 1,494,574 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000027 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000042 ( 0 hom. )
Consequence
CPED1
NM_024913.5 splice_polypyrimidine_tract, intron
NM_024913.5 splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.29
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CPED1 | NM_024913.5 | c.750-6_750-3del | splice_polypyrimidine_tract_variant, intron_variant | ENST00000310396.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CPED1 | ENST00000310396.10 | c.750-6_750-3del | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_024913.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000269 AC: 4AN: 148732Hom.: 0 Cov.: 0
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GnomAD3 exomes AF: 0.0000719 AC: 12AN: 166798Hom.: 0 AF XY: 0.0000771 AC XY: 7AN XY: 90770
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GnomAD4 exome AF: 0.0000416 AC: 56AN: 1345842Hom.: 0 AF XY: 0.0000492 AC XY: 33AN XY: 671150
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GnomAD4 genome AF: 0.0000269 AC: 4AN: 148732Hom.: 0 Cov.: 0 AF XY: 0.0000277 AC XY: 2AN XY: 72286
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ClinVar
Not reported inComputational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at