rs293813
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_178335.3(CCDC50):c.995T>A(p.Met332Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M332T) has been classified as Benign.
Frequency
Consequence
NM_178335.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC50 | NM_178335.3 | c.995T>A | p.Met332Lys | missense_variant | 7/12 | ENST00000392455.9 | |
CCDC50 | NM_174908.4 | c.467T>A | p.Met156Lys | missense_variant | 6/11 | ||
CCDC50 | XM_011512460.2 | c.*55T>A | 3_prime_UTR_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC50 | ENST00000392455.9 | c.995T>A | p.Met332Lys | missense_variant | 7/12 | 1 | NM_178335.3 | P3 | |
CCDC50 | ENST00000392456.4 | c.467T>A | p.Met156Lys | missense_variant | 6/11 | 1 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 0AN: 150700Hom.: 0 Cov.: 28 FAILED QC
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1442756Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 718778
GnomAD4 genome ? Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 150700Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0AN XY: 73414
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at