chr22-39488760-G-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_002409.5(MGAT3):āc.1413G>Cā(p.Glu471Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00014 in 1,612,318 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 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 -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MGAT3 | NM_002409.5 | c.1413G>C | p.Glu471Asp | missense_variant | 2/2 | ENST00000341184.7 | |
MGAT3 | NM_001098270.2 | c.1413G>C | p.Glu471Asp | missense_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MGAT3 | ENST00000341184.7 | c.1413G>C | p.Glu471Asp | missense_variant | 2/2 | 1 | NM_002409.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000145 AC: 22AN: 152238Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000175 AC: 43AN: 245746Hom.: 1 AF XY: 0.000202 AC XY: 27AN XY: 133444
GnomAD4 exome AF: 0.000140 AC: 205AN: 1459962Hom.: 4 Cov.: 34 AF XY: 0.000160 AC XY: 116AN XY: 726280
GnomAD4 genome AF: 0.000138 AC: 21AN: 152356Hom.: 0 Cov.: 33 AF XY: 0.000174 AC XY: 13AN XY: 74504
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 16, 2021 | The c.1413G>C (p.E471D) alteration is located in exon 2 (coding exon 1) of the MGAT3 gene. This alteration results from a G to C substitution at nucleotide position 1413, causing the glutamic acid (E) at amino acid position 471 to be replaced by an aspartic acid (D). 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