16-1434476-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001143980.3(CCDC154):c.1936G>A(p.Val646Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000342 in 1,549,956 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001143980.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCDC154 | ENST00000389176.4 | c.1936G>A | p.Val646Ile | missense_variant | Exon 17 of 17 | 5 | NM_001143980.3 | ENSP00000373828.4 | ||
PERCC1 | ENST00000640283.2 | c.*1079C>T | downstream_gene_variant | 5 | NM_001365310.2 | ENSP00000492108.2 |
Frequencies
GnomAD3 genomes AF: 0.000243 AC: 37AN: 152156Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000578 AC: 9AN: 155804Hom.: 0 AF XY: 0.0000484 AC XY: 4AN XY: 82688
GnomAD4 exome AF: 0.0000114 AC: 16AN: 1397682Hom.: 0 Cov.: 50 AF XY: 0.0000102 AC XY: 7AN XY: 689338
GnomAD4 genome AF: 0.000243 AC: 37AN: 152274Hom.: 0 Cov.: 34 AF XY: 0.000255 AC XY: 19AN XY: 74448
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1936G>A (p.V646I) alteration is located in exon 17 (coding exon 17) of the CCDC154 gene. This alteration results from a G to A substitution at nucleotide position 1936, causing the valine (V) at amino acid position 646 to be replaced by an isoleucine (I). 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