12-38848667-GGAAA-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_153634.3(CPNE8):c.187-9_187-6delTTTC variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000384 in 1,580,714 control chromosomes in the GnomAD database, including 2 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0020 ( 2 hom., cov: 32)
Exomes 𝑓: 0.00021 ( 0 hom. )
Consequence
CPNE8
NM_153634.3 splice_region, intron
NM_153634.3 splice_region, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 3.26
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 Likely_benign. Variant got -6 ACMG points.
BP6
Variant 12-38848667-GGAAA-G is Benign according to our data. Variant chr12-38848667-GGAAA-G is described in ClinVar as [Likely_benign]. Clinvar id is 2642846.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAd4 at 2 AR gene
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CPNE8 | ENST00000331366.10 | c.187-9_187-6delTTTC | splice_region_variant, intron_variant | Intron 3 of 19 | 1 | NM_153634.3 | ENSP00000329748.5 | |||
CPNE8 | ENST00000360449.3 | c.151-9_151-6delTTTC | splice_region_variant, intron_variant | Intron 3 of 19 | 2 | ENSP00000353633.3 | ||||
CPNE8 | ENST00000550863.1 | c.-297-9_-297-6delTTTC | splice_region_variant, intron_variant | Intron 3 of 7 | 4 | ENSP00000447761.1 |
Frequencies
GnomAD3 genomes AF: 0.00203 AC: 309AN: 152084Hom.: 2 Cov.: 32
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GnomAD3 exomes AF: 0.000516 AC: 113AN: 219028Hom.: 1 AF XY: 0.000378 AC XY: 45AN XY: 119072
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GnomAD4 exome AF: 0.000207 AC: 296AN: 1428512Hom.: 0 AF XY: 0.000183 AC XY: 130AN XY: 710018
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GnomAD4 genome AF: 0.00204 AC: 311AN: 152202Hom.: 2 Cov.: 32 AF XY: 0.00202 AC XY: 150AN XY: 74412
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2022 | CPNE8: BP4, BS2 - |
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at