19-11350829-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001080503.3(CCDC159):c.248G>A(p.Arg83His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000029 in 1,549,668 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. 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. R83C) has been classified 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.248G>A | p.Arg83His | missense_variant | 5/11 | ENST00000458408.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC159 | ENST00000458408.6 | c.248G>A | p.Arg83His | missense_variant | 5/11 | 5 | NM_001080503.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152134Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000130 AC: 2AN: 153654Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 81594
GnomAD4 exome AF: 0.0000272 AC: 38AN: 1397534Hom.: 0 Cov.: 32 AF XY: 0.0000232 AC XY: 16AN XY: 689336
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152134Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74318
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 09, 2024 | The c.248G>A (p.R83H) alteration is located in exon 5 (coding exon 5) of the CCDC159 gene. This alteration results from a G to A substitution at nucleotide position 248, causing the arginine (R) at amino acid position 83 to be replaced by a histidine (H). 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