2-27627394-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_024584.5(CCDC121):c.406G>T(p.Ala136Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 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. A136V) has been classified as Uncertain significance.
Frequency
Consequence
NM_024584.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
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 |
---|---|---|---|---|---|---|---|---|---|---|
CCDC121 | ENST00000324364.4 | c.406G>T | p.Ala136Ser | missense_variant | Exon 2 of 2 | 1 | NM_024584.5 | ENSP00000339087.2 | ||
CCDC121 | ENST00000394775.3 | c.892G>T | p.Ala298Ser | missense_variant | Exon 2 of 2 | 1 | ENSP00000412150.2 | |||
ENSG00000259080 | ENST00000505973.1 | n.1389-2465C>A | intron_variant | Intron 12 of 17 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 6.84e-7 AC: 1AN: 1461872Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 727232
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.892G>T (p.A298S) alteration is located in exon 2 (coding exon 2) of the CCDC121 gene. This alteration results from a G to T substitution at nucleotide position 892, causing the alanine (A) at amino acid position 298 to be replaced by a serine (S). 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
Publications
No publications associated with this variant yet.