chr7-121099908-GTTT-G
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BS1
The NM_024913.5(CPED1):c.750-5_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 0.00767 in 1,464,776 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 0.00046 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0085 ( 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 Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BS1
Variant frequency is greater than expected in population amr. gnomad4_exome allele frequency = 0.00849 (11168/1316006) while in subpopulation AMR AF= 0.0185 (672/36306). AF 95% confidence interval is 0.0173. There are 0 homozygotes in gnomad4_exome. There are 5424 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CPED1 | NM_024913.5 | c.750-5_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.750-5_750-3del | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_024913.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000457 AC: 68AN: 148686Hom.: 0 Cov.: 0
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GnomAD3 exomes AF: 0.0162 AC: 2704AN: 166798Hom.: 0 AF XY: 0.0162 AC XY: 1468AN XY: 90770
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GnomAD4 exome AF: 0.00849 AC: 11168AN: 1316006Hom.: 0 AF XY: 0.00826 AC XY: 5424AN XY: 656298
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GnomAD4 genome AF: 0.000464 AC: 69AN: 148770Hom.: 0 Cov.: 0 AF XY: 0.000442 AC XY: 32AN XY: 72360
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ClinVar
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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