12-38903226-T-C
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The NM_153634.3(CPNE8):c.98+2211A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0421 in 152,270 control chromosomes in the GnomAD database, including 168 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 0.042 ( 168 hom., cov: 33)
Consequence
CPNE8
NM_153634.3 intron
NM_153634.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.35
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 -8 ACMG points.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CPNE8 | ENST00000331366.10 | c.98+2211A>G | intron_variant | 1 | NM_153634.3 | ENSP00000329748.5 | ||||
CPNE8 | ENST00000360449.3 | c.62+4093A>G | intron_variant | 2 | ENSP00000353633.3 | |||||
CPNE8 | ENST00000550863.1 | c.-386+2916A>G | intron_variant | 4 | ENSP00000447761.1 |
Frequencies
GnomAD3 genomes AF: 0.0422 AC: 6419AN: 152152Hom.: 168 Cov.: 33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0421 AC: 6416AN: 152270Hom.: 168 Cov.: 33 AF XY: 0.0419 AC XY: 3121AN XY: 74442
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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DS_DG_spliceai
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at