chr22-39487378-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002409.5(MGAT3):āc.31A>Gā(p.Met11Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,460,536 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_002409.5 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 |
---|---|---|---|---|---|---|---|
MGAT3 | NM_002409.5 | c.31A>G | p.Met11Val | missense_variant | 2/2 | ENST00000341184.7 | |
MGAT3 | NM_001098270.2 | c.31A>G | p.Met11Val | missense_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MGAT3 | ENST00000341184.7 | c.31A>G | p.Met11Val | missense_variant | 2/2 | 1 | NM_002409.5 | P1 | |
MGAT3 | ENST00000429402.1 | c.31A>G | p.Met11Val | missense_variant | 2/2 | 4 | |||
MGAT3 | ENST00000418314.1 | c.115A>G | p.Met39Val | missense_variant | 3/3 | 4 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250516Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135368
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1460536Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 726614
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 06, 2021 | The c.31A>G (p.M11V) alteration is located in exon 2 (coding exon 1) of the MGAT3 gene. This alteration results from a A to G substitution at nucleotide position 31, causing the methionine (M) at amino acid position 11 to be replaced by a valine (V). 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