X-49063961-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001163321.4(CCDC120):c.389C>T(p.Pro130Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000332 in 1,205,207 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 6 hemizygotes in GnomAD. 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P130A) has been classified as Uncertain significance.
Frequency
Consequence
NM_001163321.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000360 AC: 4AN: 111023Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33219
GnomAD3 exomes AF: 0.0000937 AC: 16AN: 170814Hom.: 0 AF XY: 0.0000519 AC XY: 3AN XY: 57844
GnomAD4 exome AF: 0.0000329 AC: 36AN: 1094184Hom.: 0 Cov.: 31 AF XY: 0.0000167 AC XY: 6AN XY: 360036
GnomAD4 genome AF: 0.0000360 AC: 4AN: 111023Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33219
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.284C>T (p.P95L) 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 284, causing the proline (P) at amino acid position 95 to be replaced by a leucine (L). 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