chr3-127692221-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_007283.7(MGLL):c.919G>A(p.Ala307Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00473 in 1,613,696 control chromosomes in the GnomAD database, including 43 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_007283.7 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MGLL | NM_007283.7 | c.919G>A | p.Ala307Thr | missense_variant | 8/8 | ENST00000265052.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MGLL | ENST00000265052.10 | c.919G>A | p.Ala307Thr | missense_variant | 8/8 | 1 | NM_007283.7 |
Frequencies
GnomAD3 genomes ? AF: 0.00349 AC: 530AN: 151762Hom.: 5 Cov.: 31
GnomAD3 exomes AF: 0.00352 AC: 879AN: 249570Hom.: 6 AF XY: 0.00338 AC XY: 458AN XY: 135406
GnomAD4 exome AF: 0.00486 AC: 7102AN: 1461816Hom.: 38 Cov.: 35 AF XY: 0.00466 AC XY: 3391AN XY: 727214
GnomAD4 genome ? AF: 0.00349 AC: 530AN: 151880Hom.: 5 Cov.: 31 AF XY: 0.00408 AC XY: 303AN XY: 74194
ClinVar
Submissions by phenotype
MGLL-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 12, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at