19-11350873-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001080503.3(CCDC159):c.292C>T(p.Arg98Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000374 in 1,551,812 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001080503.3 missense
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC159 | NM_001080503.3 | c.292C>T | p.Arg98Trp | missense_variant | 5/11 | ENST00000458408.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC159 | ENST00000458408.6 | c.292C>T | p.Arg98Trp | missense_variant | 5/11 | 5 | NM_001080503.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000171 AC: 26AN: 152150Hom.: 1 Cov.: 31
GnomAD3 exomes AF: 0.0000709 AC: 11AN: 155088Hom.: 0 AF XY: 0.0000365 AC XY: 3AN XY: 82284
GnomAD4 exome AF: 0.0000229 AC: 32AN: 1399544Hom.: 0 Cov.: 32 AF XY: 0.0000130 AC XY: 9AN XY: 690396
GnomAD4 genome AF: 0.000171 AC: 26AN: 152268Hom.: 1 Cov.: 31 AF XY: 0.000161 AC XY: 12AN XY: 74468
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 18, 2022 | The c.292C>T (p.R98W) alteration is located in exon 5 (coding exon 5) of the CCDC159 gene. This alteration results from a C to T substitution at nucleotide position 292, causing the arginine (R) at amino acid position 98 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at