11-118257248-T-G
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_005797.4(MPZL2):c.*2A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MPZL2 | NM_005797.4 | c.*2A>C | 3_prime_UTR_variant | Exon 5 of 6 | ENST00000278937.7 | NP_005788.1 | ||
MPZL2 | NM_144765.3 | c.*2A>C | 3_prime_UTR_variant | Exon 5 of 5 | NP_658911.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MPZL2 | ENST00000278937 | c.*2A>C | 3_prime_UTR_variant | Exon 5 of 6 | 1 | NM_005797.4 | ENSP00000278937.2 | |||
MPZL2 | ENST00000438295 | c.*2A>C | 3_prime_UTR_variant | Exon 5 of 5 | 1 | ENSP00000408362.2 | ||||
MPZL2 | ENST00000528554.1 | n.413A>C | non_coding_transcript_exon_variant | Exon 1 of 2 | 3 | |||||
MPZL2 | ENST00000534175.6 | n.698A>C | non_coding_transcript_exon_variant | Exon 4 of 5 | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 29
GnomAD4 genome Cov.: 32
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
Publications
No publications associated with this variant yet.