3-127781796-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_001388315.1(MGLL):c.-43C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000149 in 1,614,058 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_001388315.1 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MGLL | NM_007283.7 | c.255C>T | p.His85His | synonymous_variant | Exon 3 of 8 | ENST00000265052.10 | NP_009214.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MGLL | ENST00000265052.10 | c.255C>T | p.His85His | synonymous_variant | Exon 3 of 8 | 1 | NM_007283.7 | ENSP00000265052.5 |
Frequencies
GnomAD3 genomes AF: 0.000316 AC: 48AN: 152134Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000646 AC: 161AN: 249208Hom.: 0 AF XY: 0.000636 AC XY: 86AN XY: 135262
GnomAD4 exome AF: 0.000132 AC: 193AN: 1461806Hom.: 1 Cov.: 31 AF XY: 0.000131 AC XY: 95AN XY: 727202
GnomAD4 genome AF: 0.000315 AC: 48AN: 152252Hom.: 0 Cov.: 32 AF XY: 0.000336 AC XY: 25AN XY: 74436
ClinVar
Submissions by phenotype
MGLL-related disorder Benign:1
This variant is classified as 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