chr22-39488821-G-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_002409.5(MGAT3):āc.1474G>Cā(p.Asp492His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000453 in 1,609,878 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MGAT3 | NM_002409.5 | c.1474G>C | p.Asp492His | missense_variant | 2/2 | ENST00000341184.7 | |
MGAT3 | NM_001098270.2 | c.1474G>C | p.Asp492His | missense_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MGAT3 | ENST00000341184.7 | c.1474G>C | p.Asp492His | missense_variant | 2/2 | 1 | NM_002409.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000276 AC: 42AN: 152210Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000583 AC: 14AN: 240116Hom.: 0 AF XY: 0.0000461 AC XY: 6AN XY: 130208
GnomAD4 exome AF: 0.0000213 AC: 31AN: 1457668Hom.: 0 Cov.: 34 AF XY: 0.0000152 AC XY: 11AN XY: 724794
GnomAD4 genome AF: 0.000276 AC: 42AN: 152210Hom.: 0 Cov.: 32 AF XY: 0.000296 AC XY: 22AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 16, 2021 | The c.1474G>C (p.D492H) 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 1474, causing the aspartic acid (D) at amino acid position 492 to be replaced by a histidine (H). 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