chr2-134338341-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_002410.5(MGAT5):c.728G>A(p.Arg243Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000682 in 1,612,946 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R243W) has been classified as Uncertain significance.
Frequency
Consequence
NM_002410.5 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 |
---|---|---|---|---|---|---|---|
MGAT5 | NM_002410.5 | c.728G>A | p.Arg243Gln | missense_variant | 6/16 | ENST00000281923.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MGAT5 | ENST00000281923.4 | c.728G>A | p.Arg243Gln | missense_variant | 6/16 | 1 | NM_002410.5 | P1 | |
MGAT5 | ENST00000409645.5 | c.728G>A | p.Arg243Gln | missense_variant | 7/17 | 5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152142Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000881 AC: 22AN: 249854Hom.: 0 AF XY: 0.000111 AC XY: 15AN XY: 135062
GnomAD4 exome AF: 0.0000698 AC: 102AN: 1460804Hom.: 0 Cov.: 31 AF XY: 0.0000853 AC XY: 62AN XY: 726680
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152142Hom.: 0 Cov.: 33 AF XY: 0.0000673 AC XY: 5AN XY: 74298
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 03, 2024 | The c.728G>A (p.R243Q) alteration is located in exon 1 (coding exon 1) of the MGAT5 gene. This alteration results from a G to A substitution at nucleotide position 728, causing the arginine (R) at amino acid position 243 to be replaced by a glutamine (Q). 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