X-134245102-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001353453.3(CCDC160):c.302C>A(p.Ser101Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001353453.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CCDC160 | NM_001353453.3 | c.302C>A | p.Ser101Tyr | missense_variant | Exon 3 of 3 | ENST00000695460.1 | NP_001340382.1 | |
CCDC160 | NM_001101357.3 | c.302C>A | p.Ser101Tyr | missense_variant | Exon 2 of 2 | NP_001094827.1 | ||
CCDC160 | NM_001393996.1 | c.302C>A | p.Ser101Tyr | missense_variant | Exon 3 of 3 | NP_001380925.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCDC160 | ENST00000695460.1 | c.302C>A | p.Ser101Tyr | missense_variant | Exon 3 of 3 | NM_001353453.3 | ENSP00000511932.1 | |||
CCDC160 | ENST00000370809.5 | c.302C>A | p.Ser101Tyr | missense_variant | Exon 2 of 2 | 5 | ENSP00000359845.4 | |||
CCDC160 | ENST00000517294.5 | c.302C>A | p.Ser101Tyr | missense_variant | Exon 3 of 3 | 5 | ENSP00000427951.1 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1074627Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 347729
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.302C>A (p.S101Y) alteration is located in exon 2 (coding exon 1) of the CCDC160 gene. This alteration results from a C to A substitution at nucleotide position 302, causing the serine (S) at amino acid position 101 to be replaced by a tyrosine (Y). 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
Publications
No publications associated with this variant yet.