3-107378280-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_032600.3(CCDC54):āc.693C>Gā(p.Ser231Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,613,960 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_032600.3 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CCDC54 | NM_032600.3 | c.693C>G | p.Ser231Arg | missense_variant | 1/1 | ENST00000261058.3 | NP_115989.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCDC54 | ENST00000261058.3 | c.693C>G | p.Ser231Arg | missense_variant | 1/1 | NM_032600.3 | ENSP00000261058 | P1 | ||
CCDC54-AS1 | ENST00000595232.2 | n.488+2305G>C | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152182Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000558 AC: 14AN: 250792Hom.: 0 AF XY: 0.0000811 AC XY: 11AN XY: 135648
GnomAD4 exome AF: 0.0000109 AC: 16AN: 1461778Hom.: 0 Cov.: 33 AF XY: 0.0000110 AC XY: 8AN XY: 727196
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152182Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 31, 2024 | The c.693C>G (p.S231R) alteration is located in exon 1 (coding exon 1) of the CCDC54 gene. This alteration results from a C to G substitution at nucleotide position 693, causing the serine (S) at amino acid position 231 to be replaced by an arginine (R). 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