chr3-127695133-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_007283.7(MGLL):c.658G>A(p.Gly220Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00103 in 1,614,136 control chromosomes in the GnomAD database, including 13 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_007283.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MGLL | NM_007283.7 | c.658G>A | p.Gly220Ser | missense_variant | Exon 7 of 8 | ENST00000265052.10 | NP_009214.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MGLL | ENST00000265052.10 | c.658G>A | p.Gly220Ser | missense_variant | Exon 7 of 8 | 1 | NM_007283.7 | ENSP00000265052.5 |
Frequencies
GnomAD3 genomes AF: 0.00147 AC: 223AN: 152172Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00311 AC: 777AN: 249442Hom.: 11 AF XY: 0.00272 AC XY: 368AN XY: 135372
GnomAD4 exome AF: 0.000988 AC: 1444AN: 1461846Hom.: 13 Cov.: 32 AF XY: 0.000939 AC XY: 683AN XY: 727232
GnomAD4 genome AF: 0.00147 AC: 224AN: 152290Hom.: 0 Cov.: 32 AF XY: 0.00168 AC XY: 125AN XY: 74464
ClinVar
Submissions by phenotype
MGLL-related disorder Benign:1
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