2-117935556-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_019044.5(CCDC93):c.1667G>A(p.Arg556Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,613,738 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R556W) has been classified as Uncertain significance.
Frequency
Consequence
NM_019044.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC93 | NM_019044.5 | c.1667G>A | p.Arg556Gln | missense_variant | 22/24 | ENST00000376300.7 | |
CCDC93 | XM_011511359.2 | c.1664G>A | p.Arg555Gln | missense_variant | 22/24 | ||
CCDC93 | XM_011511361.1 | c.1379G>A | p.Arg460Gln | missense_variant | 21/23 | ||
CCDC93 | XM_047444816.1 | c.1268G>A | p.Arg423Gln | missense_variant | 19/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC93 | ENST00000376300.7 | c.1667G>A | p.Arg556Gln | missense_variant | 22/24 | 1 | NM_019044.5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152128Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000598 AC: 15AN: 250948Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135632
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1461610Hom.: 0 Cov.: 30 AF XY: 0.00000550 AC XY: 4AN XY: 727144
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152128Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74304
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 22, 2022 | The c.1667G>A (p.R556Q) alteration is located in exon 22 (coding exon 22) of the CCDC93 gene. This alteration results from a G to A substitution at nucleotide position 1667, causing the arginine (R) at amino acid position 556 to be replaced by a glutamine (Q). 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