7-101196059-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_178176.4(MOGAT3):c.913G>A(p.Glu305Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000023 in 1,611,924 control chromosomes in the GnomAD database, including 1 homozygotes. 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 (★).
Frequency
Consequence
NM_178176.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MOGAT3 | ENST00000223114.9 | c.913G>A | p.Glu305Lys | missense_variant | Exon 7 of 7 | 1 | NM_178176.4 | ENSP00000223114.4 | ||
MOGAT3 | ENST00000379423.3 | c.710G>A | p.Arg237Gln | missense_variant | Exon 6 of 6 | 1 | ENSP00000368734.3 | |||
MOGAT3 | ENST00000440203.6 | c.999G>A | p.Pro333Pro | synonymous_variant | Exon 6 of 6 | 2 | ENSP00000403756.2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 151908Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 248398Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134670
GnomAD4 exome AF: 0.0000233 AC: 34AN: 1460016Hom.: 1 Cov.: 31 AF XY: 0.0000234 AC XY: 17AN XY: 726324
GnomAD4 genome AF: 0.0000197 AC: 3AN: 151908Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74214
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.913G>A (p.E305K) alteration is located in exon 7 (coding exon 7) of the MOGAT3 gene. This alteration results from a G to A substitution at nucleotide position 913, causing the glutamic acid (E) at amino acid position 305 to be replaced by a lysine (K). 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