2-98675089-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_012214.3(MGAT4A):c.349A>G(p.Lys117Glu) 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 1,611,958 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 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
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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.349A>G | p.Lys117Glu | missense_variant | 4/16 | ENST00000393487.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MGAT4A | ENST00000393487.6 | c.349A>G | p.Lys117Glu | missense_variant | 4/16 | 5 | NM_012214.3 | P1 | |
MGAT4A | ENST00000264968.7 | c.349A>G | p.Lys117Glu | missense_variant | 3/15 | 1 | P1 | ||
MGAT4A | ENST00000409391.1 | c.349A>G | p.Lys117Glu | missense_variant | 4/16 | 5 | P1 | ||
MGAT4A | ENST00000484936.5 | n.612A>G | non_coding_transcript_exon_variant | 4/5 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000328 AC: 5AN: 152232Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000963 AC: 24AN: 249092Hom.: 0 AF XY: 0.0000966 AC XY: 13AN XY: 134510
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1459726Hom.: 0 Cov.: 30 AF XY: 0.0000193 AC XY: 14AN XY: 726048
GnomAD4 genome ? AF: 0.0000328 AC: 5AN: 152232Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74398
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 25, 2023 | The c.349A>G (p.K117E) alteration is located in exon 4 (coding exon 3) of the MGAT4A gene. This alteration results from a A to G substitution at nucleotide position 349, causing the lysine (K) at amino acid position 117 to be replaced by a glutamic acid (E). 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