2-98678370-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_012214.3(MGAT4A):c.196G>A(p.Val66Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000761 in 1,576,584 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MGAT4A | NM_012214.3 | c.196G>A | p.Val66Met | missense_variant | 3/16 | ENST00000393487.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MGAT4A | ENST00000393487.6 | c.196G>A | p.Val66Met | missense_variant | 3/16 | 5 | NM_012214.3 | P1 | |
MGAT4A | ENST00000264968.7 | c.196G>A | p.Val66Met | missense_variant | 2/15 | 1 | P1 | ||
MGAT4A | ENST00000409391.1 | c.196G>A | p.Val66Met | missense_variant | 3/16 | 5 | P1 | ||
MGAT4A | ENST00000484936.5 | n.459G>A | non_coding_transcript_exon_variant | 3/5 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000198 AC: 3AN: 151290Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000241 AC: 6AN: 249450Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 134942
GnomAD4 exome AF: 0.00000631 AC: 9AN: 1425294Hom.: 0 Cov.: 30 AF XY: 0.00000423 AC XY: 3AN XY: 708734
GnomAD4 genome ? AF: 0.0000198 AC: 3AN: 151290Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 73844
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 16, 2021 | The c.196G>A (p.V66M) alteration is located in exon 3 (coding exon 2) of the MGAT4A gene. This alteration results from a G to A substitution at nucleotide position 196, causing the valine (V) at amino acid position 66 to be replaced by a methionine (M). 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