22-28786298-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_173510.4(CCDC117):āc.812C>Gā(p.Thr271Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,318 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 (ā ).
Frequency
Consequence
NM_173510.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC117 | NM_173510.4 | c.812C>G | p.Thr271Ser | missense_variant | 5/5 | ENST00000249064.9 | |
CCDC117 | NM_001284263.2 | c.758C>G | p.Thr253Ser | missense_variant | 4/4 | ||
CCDC117 | NM_001284264.2 | c.587C>G | p.Thr196Ser | missense_variant | 4/4 | ||
CCDC117 | NM_001284265.1 | c.416C>G | p.Thr139Ser | missense_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC117 | ENST00000249064.9 | c.812C>G | p.Thr271Ser | missense_variant | 5/5 | 1 | NM_173510.4 | P1 | |
CCDC117 | ENST00000448492.6 | c.758C>G | p.Thr253Ser | missense_variant | 4/4 | 2 | |||
CCDC117 | ENST00000421503.6 | c.587C>G | p.Thr196Ser | missense_variant | 4/4 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461318Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 726990
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 04, 2022 | The c.812C>G (p.T271S) alteration is located in exon 5 (coding exon 5) of the CCDC117 gene. This alteration results from a C to G substitution at nucleotide position 812, causing the threonine (T) at amino acid position 271 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.