chr12-85979497-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001351288.2(MGAT4C):c.1229C>A(p.Ala410Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000174 in 1,612,490 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001351288.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MGAT4C | NM_001351288.2 | c.1229C>A | p.Ala410Asp | missense_variant | 5/5 | ENST00000611864.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MGAT4C | ENST00000611864.5 | c.1229C>A | p.Ala410Asp | missense_variant | 5/5 | 5 | NM_001351288.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 151778Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000799 AC: 2AN: 250416Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135340
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1460712Hom.: 0 Cov.: 32 AF XY: 0.0000138 AC XY: 10AN XY: 726702
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 151778Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74120
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 02, 2021 | The c.1229C>A (p.A410D) alteration is located in exon 7 (coding exon 3) of the MGAT4C gene. This alteration results from a C to A substitution at nucleotide position 1229, causing the alanine (A) at amino acid position 410 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