X-141176730-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_012317.4(LDOC1):c.292G>T(p.Gly98Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000118 in 1,097,978 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_012317.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LDOC1 | NM_012317.4 | c.292G>T | p.Gly98Trp | missense_variant | Exon 1 of 1 | ENST00000370526.5 | NP_036449.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LDOC1 | ENST00000370526.5 | c.292G>T | p.Gly98Trp | missense_variant | Exon 1 of 1 | 6 | NM_012317.4 | ENSP00000359557.2 | ||
LDOC1 | ENST00000460721.1 | n.124+163G>T | intron_variant | Intron 1 of 1 | 1 | |||||
LDOC1 | ENST00000670989.1 | n.206+163G>T | intron_variant | Intron 1 of 2 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD3 exomes AF: 0.00000549 AC: 1AN: 182213Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67427
GnomAD4 exome AF: 0.0000118 AC: 13AN: 1097978Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 1AN XY: 363334
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.292G>T (p.G98W) alteration is located in exon 1 (coding exon 1) of the LDOC1 gene. This alteration results from a G to T substitution at nucleotide position 292, causing the glycine (G) at amino acid position 98 to be replaced by a tryptophan (W). 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