X-49063927-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_001163321.4(CCDC120):c.355C>T(p.Arg119Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000306 in 1,207,402 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 16 hemizygotes in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001163321.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000270 AC: 3AN: 111176Hom.: 0 Cov.: 23 AF XY: 0.0000300 AC XY: 1AN XY: 33362
GnomAD3 exomes AF: 0.0000172 AC: 3AN: 174498Hom.: 0 AF XY: 0.0000163 AC XY: 1AN XY: 61406
GnomAD4 exome AF: 0.0000310 AC: 34AN: 1096226Hom.: 0 Cov.: 31 AF XY: 0.0000415 AC XY: 15AN XY: 361810
GnomAD4 genome AF: 0.0000270 AC: 3AN: 111176Hom.: 0 Cov.: 23 AF XY: 0.0000300 AC XY: 1AN XY: 33362
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.250C>T (p.R84W) alteration is located in exon 5 (coding exon 3) of the CCDC120 gene. This alteration results from a C to T substitution at nucleotide position 250, causing the arginine (R) at amino acid position 84 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