chr18-74353309-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001174123.2(C18orf63):c.1042G>A(p.Ala348Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000348 in 1,536,380 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001174123.2 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 |
---|---|---|---|---|---|---|---|
C18orf63 | NM_001174123.2 | c.1042G>A | p.Ala348Thr | missense_variant | 12/14 | ENST00000579455.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C18orf63 | ENST00000579455.2 | c.1042G>A | p.Ala348Thr | missense_variant | 12/14 | 1 | NM_001174123.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000316 AC: 48AN: 151988Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000194 AC: 27AN: 138922Hom.: 0 AF XY: 0.000187 AC XY: 14AN XY: 75030
GnomAD4 exome AF: 0.000352 AC: 487AN: 1384274Hom.: 0 Cov.: 35 AF XY: 0.000328 AC XY: 224AN XY: 683056
GnomAD4 genome ? AF: 0.000316 AC: 48AN: 152106Hom.: 0 Cov.: 32 AF XY: 0.000350 AC XY: 26AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 13, 2021 | The c.1042G>A (p.A348T) alteration is located in exon 12 (coding exon 11) of the C18orf63 gene. This alteration results from a G to A substitution at nucleotide position 1042, causing the alanine (A) at amino acid position 348 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