chr2-98635248-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_012214.3(MGAT4A):c.1442G>A(p.Arg481Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000023 in 1,609,450 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_012214.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MGAT4A | NM_012214.3 | c.1442G>A | p.Arg481Gln | missense_variant | 14/16 | ENST00000393487.6 | |
MGAT4A | NM_001160154.2 | c.1058G>A | p.Arg353Gln | missense_variant | 11/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MGAT4A | ENST00000393487.6 | c.1442G>A | p.Arg481Gln | missense_variant | 14/16 | 5 | NM_012214.3 | P1 | |
MGAT4A | ENST00000264968.7 | c.1442G>A | p.Arg481Gln | missense_variant | 13/15 | 1 | P1 | ||
MGAT4A | ENST00000409391.1 | c.1442G>A | p.Arg481Gln | missense_variant | 14/16 | 5 | P1 | ||
MGAT4A | ENST00000414521.6 | c.1058G>A | p.Arg353Gln | missense_variant | 11/13 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000920 AC: 14AN: 152162Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000322 AC: 8AN: 248364Hom.: 0 AF XY: 0.0000298 AC XY: 4AN XY: 134352
GnomAD4 exome AF: 0.0000158 AC: 23AN: 1457170Hom.: 0 Cov.: 28 AF XY: 0.0000179 AC XY: 13AN XY: 725032
GnomAD4 genome ? AF: 0.0000919 AC: 14AN: 152280Hom.: 0 Cov.: 31 AF XY: 0.0000940 AC XY: 7AN XY: 74468
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 25, 2022 | The c.1442G>A (p.R481Q) alteration is located in exon 14 (coding exon 13) of the MGAT4A gene. This alteration results from a G to A substitution at nucleotide position 1442, causing the arginine (R) at amino acid position 481 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