chr20-35626328-C-A
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_152925.3(CPNE1):c.1527G>T(p.Leu509=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000367 in 1,614,072 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00022 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00038 ( 3 hom. )
Consequence
CPNE1
NM_152925.3 synonymous
NM_152925.3 synonymous
Scores
1
1
Clinical Significance
Conservation
PhyloP100: -0.105
Genes affected
CPNE1 (HGNC:2314): (copine 1) Calcium-dependent membrane-binding proteins may regulate molecular events at the interface of the cell membrane and cytoplasm. This gene encodes a calcium-dependent protein that also contains two N-terminal type II C2 domains and an integrin A domain-like sequence in the C-terminus. However, the encoded protein does not contain a predicted signal sequence or transmembrane domains. This protein has a broad tissue distribution and it may function in membrane trafficking. This gene and the gene for RNA binding motif protein 12 overlap at map location 20q11.21. Alternate splicing results in multiple transcript variants encoding different proteins. [provided by RefSeq, Aug 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.32).
BP6
Variant 20-35626328-C-A is Benign according to our data. Variant chr20-35626328-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 3250608.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.105 with no splicing effect.
BS2
High Homozygotes in GnomAdExome4 at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CPNE1 | NM_152925.3 | c.1527G>T | p.Leu509= | synonymous_variant | 16/16 | ENST00000397443.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CPNE1 | ENST00000397443.7 | c.1527G>T | p.Leu509= | synonymous_variant | 16/16 | 5 | NM_152925.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000224 AC: 34AN: 152082Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.000808 AC: 203AN: 251322Hom.: 2 AF XY: 0.00108 AC XY: 147AN XY: 135866
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GnomAD4 exome AF: 0.000382 AC: 559AN: 1461872Hom.: 3 Cov.: 32 AF XY: 0.000529 AC XY: 385AN XY: 727242
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GnomAD4 genome AF: 0.000223 AC: 34AN: 152200Hom.: 1 Cov.: 32 AF XY: 0.000309 AC XY: 23AN XY: 74410
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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 | Jun 01, 2024 | CPNE1: BP4, BP7, BS2 - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at