rs10506131
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_153634.3(CPNE8):c.99-8272T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0403 in 152,186 control chromosomes in the GnomAD database, including 298 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 0.040 ( 298 hom., cov: 32)
Consequence
CPNE8
NM_153634.3 intron
NM_153634.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0540
Genes affected
CPNE8 (HGNC:23498): (copine 8) Calcium-dependent membrane-binding proteins may regulate molecular events at the interface of the cell membrane and cytoplasm. This gene is one of several genes that encode a calcium-dependent protein containing two N-terminal type II C2 domains and an integrin A domain-like sequence in the C-terminus. [provided by RefSeq, Jul 2008]
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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=-0.88).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CPNE8 | NM_153634.3 | c.99-8272T>C | intron_variant | ENST00000331366.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CPNE8 | ENST00000331366.10 | c.99-8272T>C | intron_variant | 1 | NM_153634.3 | P1 | |||
CPNE8 | ENST00000360449.3 | c.63-8272T>C | intron_variant | 2 | |||||
CPNE8 | ENST00000550863.1 | c.-385-8272T>C | intron_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0403 AC: 6122AN: 152068Hom.: 296 Cov.: 32
GnomAD3 genomes
?
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0403 AC: 6138AN: 152186Hom.: 298 Cov.: 32 AF XY: 0.0404 AC XY: 3010AN XY: 74424
GnomAD4 genome
?
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6138
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152186
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32
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3010
AN XY:
74424
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28
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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