16-1436034-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.1540G>A(p.Val514Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000226 in 1,550,322 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.1540G>A | p.Val514Met | missense_variant | Exon 14 of 17 | 5 | NM_001143980.3 | ENSP00000373828.4 | ||
CCDC154 | ENST00000409671.5 | c.1105G>A | p.Val369Met | missense_variant | Exon 13 of 16 | 1 | ENSP00000386744.1 | |||
CCDC154 | ENST00000483702.5 | n.284+411G>A | intron_variant | Intron 3 of 5 | 3 | ENSP00000456484.1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152196Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000321 AC: 5AN: 155960Hom.: 0 AF XY: 0.0000242 AC XY: 2AN XY: 82774
GnomAD4 exome AF: 0.0000207 AC: 29AN: 1398008Hom.: 0 Cov.: 31 AF XY: 0.0000232 AC XY: 16AN XY: 689524
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152314Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74474
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1540G>A (p.V514M) alteration is located in exon 14 (coding exon 14) of the CCDC154 gene. This alteration results from a G to A substitution at nucleotide position 1540, causing the valine (V) at amino acid position 514 to be replaced by a methionine (M). 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