8-81443446-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The ENST00000519260.1(PMP2):āc.178A>Gā(p.Met60Val) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000188 in 1,595,932 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/14 in silico tools predict a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M60I) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000519260.1 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PMP2 | NM_002677.5 | c.351A>G | p.Glu117= | splice_region_variant, synonymous_variant | 4/4 | ENST00000256103.3 | |
PMP2 | NM_001348381.2 | c.178A>G | p.Met60Val | missense_variant, splice_region_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PMP2 | ENST00000519260.1 | c.178A>G | p.Met60Val | missense_variant, splice_region_variant | 3/3 | 1 | |||
PMP2 | ENST00000256103.3 | c.351A>G | p.Glu117= | splice_region_variant, synonymous_variant | 4/4 | 1 | NM_002677.5 | P1 | |
ENST00000524085.2 | n.298+3353T>C | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152126Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000416 AC: 1AN: 240164Hom.: 0 AF XY: 0.00000769 AC XY: 1AN XY: 130120
GnomAD4 exome AF: 0.00000139 AC: 2AN: 1443806Hom.: 0 Cov.: 26 AF XY: 0.00000139 AC XY: 1AN XY: 718512
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152126Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74302
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 04, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at