chr17-44901102-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.
The NM_213607.3(CCDC103):c.104G>A(p.Arg35Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000106 in 1,606,290 control chromosomes in the GnomAD database, including 2 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R35P) has been classified as Uncertain significance.
Frequency
Consequence
NM_213607.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC103 | NM_213607.3 | c.104G>A | p.Arg35Gln | missense_variant | 2/4 | ENST00000417826.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC103 | ENST00000417826.3 | c.104G>A | p.Arg35Gln | missense_variant | 2/4 | 1 | NM_213607.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000315 AC: 48AN: 152216Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000140 AC: 34AN: 243336Hom.: 1 AF XY: 0.000106 AC XY: 14AN XY: 132010
GnomAD4 exome AF: 0.0000846 AC: 123AN: 1454074Hom.: 2 Cov.: 31 AF XY: 0.0000705 AC XY: 51AN XY: 723606
GnomAD4 genome ? AF: 0.000315 AC: 48AN: 152216Hom.: 0 Cov.: 33 AF XY: 0.000377 AC XY: 28AN XY: 74358
ClinVar
Submissions by phenotype
Primary ciliary dyskinesia 17 Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Jan 20, 2022 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 28, 2017 | 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. - |
Primary ciliary dyskinesia Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Sep 06, 2022 | This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 35 of the CCDC103 protein (p.Arg35Gln). This variant is present in population databases (rs587783065, gnomAD 0.08%), including at least one homozygous and/or hemizygous individual. This variant has not been reported in the literature in individuals affected with CCDC103-related conditions. ClinVar contains an entry for this variant (Variation ID: 888962). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at