19-39335292-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_004877.4(GMFG):c.119G>A(p.Arg40Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000192 in 1,565,782 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R40G) has been classified as Uncertain significance.
Frequency
Consequence
NM_004877.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GMFG | NM_004877.4 | c.119G>A | p.Arg40Gln | missense_variant | Exon 3 of 7 | ENST00000597595.6 | NP_004868.1 | |
GMFG | NM_001411106.1 | c.20G>A | p.Arg7Gln | missense_variant | Exon 3 of 7 | NP_001398035.1 | ||
GMFG | NM_001301008.2 | c.-5G>A | 5_prime_UTR_variant | Exon 2 of 6 | NP_001287937.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152162Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000189 AC: 4AN: 211998Hom.: 0 AF XY: 0.00000894 AC XY: 1AN XY: 111904
GnomAD4 exome AF: 0.0000184 AC: 26AN: 1413620Hom.: 0 Cov.: 30 AF XY: 0.0000143 AC XY: 10AN XY: 697086
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152162Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74328
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.119G>A (p.R40Q) alteration is located in exon 3 (coding exon 3) of the GMFG gene. This alteration results from a G to A substitution at nucleotide position 119, causing the arginine (R) at amino acid position 40 to be replaced by a glutamine (Q). 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