rs370925743
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6BP7
The NM_005797.4(MPZL2):c.423C>T(p.Ser141Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000942 in 1,613,780 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_005797.4 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MPZL2 | NM_005797.4 | c.423C>T | p.Ser141Ser | synonymous_variant | Exon 3 of 6 | ENST00000278937.7 | NP_005788.1 | |
MPZL2 | NM_144765.3 | c.423C>T | p.Ser141Ser | synonymous_variant | Exon 3 of 5 | NP_658911.1 | ||
MPZL2 | XM_047426229.1 | c.372+51C>T | intron_variant | Intron 3 of 3 | XP_047282185.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000197 AC: 30AN: 152062Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000120 AC: 30AN: 250786Hom.: 0 AF XY: 0.000140 AC XY: 19AN XY: 135580
GnomAD4 exome AF: 0.0000842 AC: 123AN: 1461600Hom.: 0 Cov.: 31 AF XY: 0.0000894 AC XY: 65AN XY: 727100
GnomAD4 genome AF: 0.000191 AC: 29AN: 152180Hom.: 0 Cov.: 32 AF XY: 0.000202 AC XY: 15AN XY: 74408
ClinVar
Submissions by phenotype
MPZL2-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