17-82101689-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001394669.1(CCDC57):c.3077T>C(p.Met1026Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000108 in 1,604,620 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001394669.1 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 |
---|---|---|---|---|---|---|---|
CCDC57 | NM_001394669.1 | c.3077T>C | p.Met1026Thr | missense_variant | 19/19 | ENST00000694881.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC57 | ENST00000694881.1 | c.3077T>C | p.Met1026Thr | missense_variant | 19/19 | NM_001394669.1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152234Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000580 AC: 14AN: 241506Hom.: 0 AF XY: 0.0000531 AC XY: 7AN XY: 131816
GnomAD4 exome AF: 0.000115 AC: 167AN: 1452386Hom.: 4 Cov.: 30 AF XY: 0.000113 AC XY: 82AN XY: 722674
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152234Hom.: 0 Cov.: 34 AF XY: 0.0000403 AC XY: 3AN XY: 74374
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 14, 2023 | The c.2741T>C (p.M914T) alteration is located in exon 17 (coding exon 16) of the CCDC57 gene. This alteration results from a T to C substitution at nucleotide position 2741, causing the methionine (M) at amino acid position 914 to be replaced by a threonine (T). 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