chr12-85980130-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001351288.2(MGAT4C):c.596G>T(p.Arg199Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00000929 in 1,613,778 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001351288.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MGAT4C | NM_001351288.2 | c.596G>T | p.Arg199Leu | missense_variant | Exon 5 of 5 | ENST00000611864.5 | NP_001338217.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152024Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 251036Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135672
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461754Hom.: 0 Cov.: 32 AF XY: 0.00000688 AC XY: 5AN XY: 727174
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152024Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74268
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.596G>T (p.R199L) alteration is located in exon 7 (coding exon 3) of the MGAT4C gene. This alteration results from a G to T substitution at nucleotide position 596, causing the arginine (R) at amino acid position 199 to be replaced by a leucine (L). 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