7-134137083-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_144648.3(LRGUK):c.358C>T(p.Arg120Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000496 in 1,613,324 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 (★).
Frequency
Consequence
NM_144648.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LRGUK | ENST00000285928.3 | c.358C>T | p.Arg120Cys | missense_variant | Exon 2 of 20 | 1 | NM_144648.3 | ENSP00000285928.2 | ||
LRGUK | ENST00000695542.2 | c.358C>T | p.Arg120Cys | missense_variant | Exon 2 of 16 | ENSP00000511999.1 | ||||
LRGUK | ENST00000645682.1 | c.358C>T | p.Arg120Cys | missense_variant | Exon 2 of 16 | ENSP00000495637.1 | ||||
LRGUK | ENST00000473068.1 | n.368C>T | non_coding_transcript_exon_variant | Exon 2 of 4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152146Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000761 AC: 19AN: 249590Hom.: 0 AF XY: 0.0000890 AC XY: 12AN XY: 134822
GnomAD4 exome AF: 0.0000500 AC: 73AN: 1461060Hom.: 0 Cov.: 30 AF XY: 0.0000482 AC XY: 35AN XY: 726702
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152264Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74444
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.358C>T (p.R120C) alteration is located in exon 2 (coding exon 2) of the LRGUK gene. This alteration results from a C to T substitution at nucleotide position 358, causing the arginine (R) at amino acid position 120 to be replaced by a cysteine (C). 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