3-191329707-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_178335.3(CCDC50):c.33G>A(p.Leu11Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,610,392 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_178335.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCDC50 | ENST00000392455.9 | c.33G>A | p.Leu11Leu | synonymous_variant | Exon 1 of 12 | 1 | NM_178335.3 | ENSP00000376249.4 | ||
CCDC50 | ENST00000392456.4 | c.33G>A | p.Leu11Leu | synonymous_variant | Exon 1 of 11 | 1 | ENSP00000376250.4 | |||
UTS2B | ENST00000340524.10 | c.-665+707C>T | intron_variant | Intron 1 of 8 | 2 | NM_198152.5 | ENSP00000340526.5 | |||
UTS2B | ENST00000432514.5 | c.-832+707C>T | intron_variant | Intron 1 of 6 | 5 | ENSP00000401028.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152192Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000420 AC: 1AN: 238330Hom.: 0 AF XY: 0.00000770 AC XY: 1AN XY: 129942
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1458200Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 725052
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152192Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74358
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
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Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this variant does not alter splicing; Has not been previously published as pathogenic or benign to our knowledge -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at