chr2-98639948-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_012214.3(MGAT4A):c.1182G>A(p.Ala394=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000258 in 1,613,994 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 Benign (★).
Frequency
Genomes: 𝑓 0.0011 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00017 ( 0 hom. )
Consequence
MGAT4A
NM_012214.3 synonymous
NM_012214.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0970
Genes affected
MGAT4A (HGNC:7047): (alpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase A) This gene encodes a key glycosyltransferase that regulates the formation of tri- and multiantennary branching structures in the Golgi apparatus. The encoded protein, in addition to the related isoenzyme B, catalyzes the transfer of N-acetylglucosamine (GlcNAc) from UDP-GlcNAc in a beta-1,4 linkage to the Man-alpha-1,3-Man-beta-1,4-GlcNAc arm of R-Man-alpha-1,6(GlcNAc-beta-1,2-Man-alpha-1,3)Man-beta-1,4-GlcNAc-beta-1,4-GlcNAc-beta-1-Asn. The encoded protein may play a role in regulating the availability of serum glycoproteins, oncogenesis, and differentiation. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.4).
BP6
?
Variant 2-98639948-C-T is Benign according to our data. Variant chr2-98639948-C-T is described in ClinVar as [Benign]. Clinvar id is 718738.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.097 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MGAT4A | NM_012214.3 | c.1182G>A | p.Ala394= | synonymous_variant | 12/16 | ENST00000393487.6 | |
MGAT4A | NM_001160154.2 | c.798G>A | p.Ala266= | synonymous_variant | 9/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MGAT4A | ENST00000393487.6 | c.1182G>A | p.Ala394= | synonymous_variant | 12/16 | 5 | NM_012214.3 | P1 | |
MGAT4A | ENST00000264968.7 | c.1182G>A | p.Ala394= | synonymous_variant | 11/15 | 1 | P1 | ||
MGAT4A | ENST00000409391.1 | c.1182G>A | p.Ala394= | synonymous_variant | 12/16 | 5 | P1 | ||
MGAT4A | ENST00000414521.6 | c.798G>A | p.Ala266= | synonymous_variant | 9/13 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00112 AC: 171AN: 152136Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000426 AC: 107AN: 251256Hom.: 0 AF XY: 0.000317 AC XY: 43AN XY: 135816
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GnomAD4 exome AF: 0.000168 AC: 246AN: 1461740Hom.: 0 Cov.: 31 AF XY: 0.000150 AC XY: 109AN XY: 727172
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 13, 2017 | - - |
Computational scores
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Benign
Cadd
Benign
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Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at