chr17-82163331-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001394669.1(CCDC57):c.1909G>A(p.Gly637Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000403 in 1,613,696 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 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.1909G>A | p.Gly637Arg | missense_variant | 13/19 | ENST00000694881.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC57 | ENST00000694881.1 | c.1909G>A | p.Gly637Arg | missense_variant | 13/19 | NM_001394669.1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000658 AC: 10AN: 152038Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000602 AC: 15AN: 249198Hom.: 0 AF XY: 0.0000592 AC XY: 8AN XY: 135188
GnomAD4 exome AF: 0.0000376 AC: 55AN: 1461540Hom.: 0 Cov.: 31 AF XY: 0.0000426 AC XY: 31AN XY: 727056
GnomAD4 genome ? AF: 0.0000657 AC: 10AN: 152156Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74426
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 23, 2023 | The c.1909G>A (p.G637R) alteration is located in exon 13 (coding exon 12) of the CCDC57 gene. This alteration results from a G to A substitution at nucleotide position 1909, causing the glycine (G) at amino acid position 637 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