2-130339144-C-T
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_032357.4(CCDC115):c.519G>A(p.Lys173=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0044 in 1,614,026 control chromosomes in the GnomAD database, including 281 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.023 ( 135 hom., cov: 33)
Exomes 𝑓: 0.0025 ( 146 hom. )
Consequence
CCDC115
NM_032357.4 synonymous
NM_032357.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.04
Genes affected
CCDC115 (HGNC:28178): (coiled-coil domain containing 115) The protein encoded by this gene has been observed to localize to the endoplasmic reticulum (ER)-Golgi intermediate compartment (ERGIC) and coat protein complex I (COPI) vesicles in some human cells. The encoded protein shares some homology with the yeast V-ATPase assembly factor Vma22p, and the orthologous protein in mouse promotes cell proliferation and suppresses cell death. Defects in this gene are a cause of congenital disorder of glycosylation, type IIo in humans. [provided by RefSeq, Mar 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.55).
BP6
Variant 2-130339144-C-T is Benign according to our data. Variant chr2-130339144-C-T is described in ClinVar as [Benign]. Clinvar id is 785008.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=3.04 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0778 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CCDC115 | NM_032357.4 | c.519G>A | p.Lys173= | synonymous_variant | 5/5 | ENST00000259229.7 | NP_115733.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCDC115 | ENST00000259229.7 | c.519G>A | p.Lys173= | synonymous_variant | 5/5 | 1 | NM_032357.4 | ENSP00000259229 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0230 AC: 3500AN: 152144Hom.: 134 Cov.: 33
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GnomAD3 exomes AF: 0.00586 AC: 1473AN: 251270Hom.: 64 AF XY: 0.00420 AC XY: 570AN XY: 135812
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GnomAD4 exome AF: 0.00246 AC: 3594AN: 1461764Hom.: 146 Cov.: 30 AF XY: 0.00215 AC XY: 1564AN XY: 727184
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GnomAD4 genome AF: 0.0231 AC: 3512AN: 152262Hom.: 135 Cov.: 33 AF XY: 0.0225 AC XY: 1677AN XY: 74450
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 29, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 05, 2021 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
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