4-15516648-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6BP7
The NM_001378615.1(CC2D2A):c.1041C>T(p.Asp347Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000667 in 1,612,664 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001378615.1 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CC2D2A | NM_001378615.1 | c.1041C>T | p.Asp347Asp | synonymous_variant | Exon 11 of 37 | ENST00000424120.6 | NP_001365544.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000644 AC: 98AN: 152142Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000894 AC: 222AN: 248248Hom.: 0 AF XY: 0.00114 AC XY: 153AN XY: 134690
GnomAD4 exome AF: 0.000670 AC: 978AN: 1460404Hom.: 1 Cov.: 30 AF XY: 0.000776 AC XY: 564AN XY: 726452
GnomAD4 genome AF: 0.000644 AC: 98AN: 152260Hom.: 0 Cov.: 32 AF XY: 0.000699 AC XY: 52AN XY: 74438
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:2
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CC2D2A: BP4, BP7 -
Joubert syndrome 9 Uncertain:2
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. -
This variant was classified as: Uncertain significance. The following ACMG criteria were applied in classifying this variant: PM2,PP3,PP4. -
Retinal dystrophy Uncertain:1
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Meckel syndrome, type 6 Uncertain:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. -
CC2D2A-related disorder Uncertain:1
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Meckel-Gruber syndrome;C0431399:Joubert syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at