rs117419007
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BS1BS2
The NM_017950.4(CCDC40):c.630C>T(p.Ser210Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00592 in 1,613,620 control chromosomes in the GnomAD database, including 46 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_017950.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CCDC40 | NM_017950.4 | c.630C>T | p.Ser210Ser | synonymous_variant | Exon 4 of 20 | ENST00000397545.9 | NP_060420.2 | |
CCDC40 | NM_001243342.2 | c.630C>T | p.Ser210Ser | synonymous_variant | Exon 4 of 18 | NP_001230271.1 | ||
CCDC40 | NM_001330508.2 | c.630C>T | p.Ser210Ser | synonymous_variant | Exon 4 of 11 | NP_001317437.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00478 AC: 727AN: 152178Hom.: 5 Cov.: 33
GnomAD3 exomes AF: 0.00598 AC: 1484AN: 248064Hom.: 8 AF XY: 0.00603 AC XY: 813AN XY: 134846
GnomAD4 exome AF: 0.00604 AC: 8821AN: 1461324Hom.: 41 Cov.: 33 AF XY: 0.00604 AC XY: 4388AN XY: 726986
GnomAD4 genome AF: 0.00478 AC: 728AN: 152296Hom.: 5 Cov.: 33 AF XY: 0.00494 AC XY: 368AN XY: 74478
ClinVar
Submissions by phenotype
not specified Benign:2
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Primary ciliary dyskinesia Benign:2
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This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
not provided Benign:2
CCDC40: BP4, BP7, BS2 -
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Primary ciliary dyskinesia 15 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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at