7-77260136-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_020879.3(CCDC146):c.886G>A(p.Gly296Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000372 in 1,613,778 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020879.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC146 | NM_020879.3 | c.886G>A | p.Gly296Ser | missense_variant | 8/19 | ENST00000285871.5 | |
LOC102723791 | XR_927688.3 | n.380-2881C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC146 | ENST00000285871.5 | c.886G>A | p.Gly296Ser | missense_variant | 8/19 | 1 | NM_020879.3 | P1 | |
CCDC146 | ENST00000415740.6 | n.169G>A | non_coding_transcript_exon_variant | 1/11 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 151970Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251430Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135890
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461808Hom.: 0 Cov.: 33 AF XY: 0.00000275 AC XY: 2AN XY: 727200
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 151970Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74226
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 18, 2022 | The c.886G>A (p.G296S) alteration is located in exon 8 (coding exon 7) of the CCDC146 gene. This alteration results from a G to A substitution at nucleotide position 886, causing the glycine (G) at amino acid position 296 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