2-27312494-C-G
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_002437.5(MPV17):āc.375G>Cā(p.Arg125=) variant causes a splice region, synonymous change. The variant allele was found at a frequency of 0.000000684 in 1,461,670 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. R125R) has been classified as Likely pathogenic.
Frequency
Consequence
NM_002437.5 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MPV17 | NM_002437.5 | c.375G>C | p.Arg125= | splice_region_variant, synonymous_variant | 5/8 | ENST00000380044.6 | |
MPV17 | XM_005264326.5 | c.375G>C | p.Arg125= | splice_region_variant, synonymous_variant | 5/8 | ||
MPV17 | XM_017004151.2 | c.327G>C | p.Arg109= | splice_region_variant, synonymous_variant | 5/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MPV17 | ENST00000380044.6 | c.375G>C | p.Arg125= | splice_region_variant, synonymous_variant | 5/8 | 1 | NM_002437.5 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461670Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 727128
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at