chr14-49620844-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBS1_Supporting
The NM_002408.4(MGAT2):c.-425C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000437 in 635,670 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002408.4 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MGAT2 | ENST00000305386 | c.-425C>T | 5_prime_UTR_variant | Exon 1 of 1 | NM_002408.4 | ENSP00000307423.2 | ||||
ENSG00000258377 | ENST00000555043.1 | n.2440G>A | non_coding_transcript_exon_variant | Exon 2 of 2 | 2 | |||||
RPL36AL | ENST00000298289.7 | c.-319G>A | upstream_gene_variant | 1 | NM_001001.5 | ENSP00000346012.5 |
Frequencies
GnomAD3 genomes AF: 0.000342 AC: 52AN: 152232Hom.: 1 Cov.: 34
GnomAD4 exome AF: 0.000468 AC: 226AN: 483320Hom.: 1 Cov.: 0 AF XY: 0.000512 AC XY: 133AN XY: 259708
GnomAD4 genome AF: 0.000341 AC: 52AN: 152350Hom.: 1 Cov.: 34 AF XY: 0.000282 AC XY: 21AN XY: 74504
ClinVar
Submissions by phenotype
MGAT2-congenital disorder of glycosylation Uncertain:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at