rs4609139
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_024913.5(CPED1):c.2311-2466A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 151,828 control chromosomes in the GnomAD database, including 7,702 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 0.31 ( 7702 hom., cov: 32)
Consequence
CPED1
NM_024913.5 intron
NM_024913.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.539
Genes affected
CPED1 (HGNC:26159): (cadherin like and PC-esterase domain containing 1) Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.86).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CPED1 | NM_024913.5 | c.2311-2466A>T | intron_variant | ENST00000310396.10 | NP_079189.4 | |||
CPED1 | XM_024446941.2 | c.1798-2466A>T | intron_variant | XP_024302709.1 | ||||
LOC124901735 | XR_007060494.1 | n.64+2900T>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CPED1 | ENST00000310396.10 | c.2311-2466A>T | intron_variant | 1 | NM_024913.5 | ENSP00000309772.5 |
Frequencies
GnomAD3 genomes AF: 0.312 AC: 47363AN: 151710Hom.: 7691 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.312 AC: 47402AN: 151828Hom.: 7702 Cov.: 32 AF XY: 0.309 AC XY: 22902AN XY: 74178
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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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