X-49062515-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_001163321.4(CCDC120):c.202C>T(p.Arg68Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000132 in 1,210,434 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 5 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign 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 -5 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000534 AC: 6AN: 112461Hom.: 0 Cov.: 24 AF XY: 0.0000578 AC XY: 2AN XY: 34623
GnomAD3 exomes AF: 0.0000220 AC: 4AN: 181481Hom.: 0 AF XY: 0.0000150 AC XY: 1AN XY: 66717
GnomAD4 exome AF: 0.00000911 AC: 10AN: 1097973Hom.: 0 Cov.: 33 AF XY: 0.00000826 AC XY: 3AN XY: 363355
GnomAD4 genome AF: 0.0000534 AC: 6AN: 112461Hom.: 0 Cov.: 24 AF XY: 0.0000578 AC XY: 2AN XY: 34623
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.97C>T (p.R33W) alteration is located in exon 4 (coding exon 2) of the CCDC120 gene. This alteration results from a C to T substitution at nucleotide position 97, causing the arginine (R) at amino acid position 33 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