chr4-24831546-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_001395273.1(CCDC149):c.910G>A(p.Glu304Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,613,932 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001395273.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CCDC149 | NM_001395273.1 | c.910G>A | p.Glu304Lys | missense_variant | Exon 9 of 13 | ENST00000635206.3 | NP_001382202.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCDC149 | ENST00000635206.3 | c.910G>A | p.Glu304Lys | missense_variant | Exon 9 of 13 | 5 | NM_001395273.1 | ENSP00000488929.2 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152102Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251298Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135808
GnomAD4 exome AF: 0.0000109 AC: 16AN: 1461830Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 727210
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152102Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74292
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.925G>A (p.E309K) alteration is located in exon 10 (coding exon 9) of the CCDC149 gene. This alteration results from a G to A substitution at nucleotide position 925, causing the glutamic acid (E) at amino acid position 309 to be replaced by a lysine (K). 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