chr12-64318729-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001170633.2(C12orf56):c.740G>A(p.Gly247Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000294 in 1,536,928 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001170633.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
C12orf56 | ENST00000543942.7 | c.740G>A | p.Gly247Glu | missense_variant | Exon 4 of 13 | 5 | NM_001170633.2 | ENSP00000446101.2 | ||
C12orf56 | ENST00000333722.9 | c.488+12231G>A | intron_variant | Intron 3 of 10 | 1 | ENSP00000329698.5 | ||||
C12orf56 | ENST00000543259.1 | c.450-5977G>A | intron_variant | Intron 3 of 4 | 4 | ENSP00000443341.1 | ||||
ENSG00000243024 | ENST00000535684.6 | n.324-70304C>T | intron_variant | Intron 2 of 4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000198 AC: 30AN: 151872Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000201 AC: 28AN: 139482Hom.: 0 AF XY: 0.000227 AC XY: 17AN XY: 74794
GnomAD4 exome AF: 0.000305 AC: 422AN: 1384938Hom.: 0 Cov.: 30 AF XY: 0.000303 AC XY: 207AN XY: 683396
GnomAD4 genome AF: 0.000197 AC: 30AN: 151990Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74304
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.740G>A (p.G247E) alteration is located in exon 4 (coding exon 4) of the C12orf56 gene. This alteration results from a G to A substitution at nucleotide position 740, causing the glycine (G) at amino acid position 247 to be replaced by a glutamic acid (E). 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