rs183413880
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_181426.2(CCDC39):c.1073C>T(p.Thr358Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00495 in 1,539,912 control chromosomes in the GnomAD database, including 28 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_181426.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00330 AC: 502AN: 151930Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00382 AC: 585AN: 153056Hom.: 6 AF XY: 0.00397 AC XY: 319AN XY: 80256
GnomAD4 exome AF: 0.00513 AC: 7125AN: 1387864Hom.: 26 Cov.: 28 AF XY: 0.00513 AC XY: 3514AN XY: 684612
GnomAD4 genome AF: 0.00330 AC: 502AN: 152048Hom.: 2 Cov.: 32 AF XY: 0.00320 AC XY: 238AN XY: 74340
ClinVar
Submissions by phenotype
not provided Benign:5
This variant is associated with the following publications: (PMID: 31213628) -
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CCDC39: BP4, BS2 -
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Primary ciliary dyskinesia 14 Uncertain:1Benign:2
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This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -
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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at