rs373729655
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PM5PP3_Moderate
The NM_001164507.2(NEB):c.403G>C(p.Val135Leu) variant causes a missense, splice region change. The variant was absent in control chromosomes in GnomAD project. 2/3 splice prediction tools predicting alterations to normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V135I) has been classified as Uncertain significance.
Frequency
Consequence
NM_001164507.2 missense, splice_region
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 |
---|---|---|---|---|---|---|---|
NEB | NM_001164507.2 | c.403G>C | p.Val135Leu | missense_variant, splice_region_variant | 7/182 | ENST00000427231.7 | |
NEB | NM_001164508.2 | c.403G>C | p.Val135Leu | missense_variant, splice_region_variant | 7/182 | ENST00000397345.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.403G>C | p.Val135Leu | missense_variant, splice_region_variant | 7/182 | 5 | NM_001164508.2 | P5 | |
NEB | ENST00000427231.7 | c.403G>C | p.Val135Leu | missense_variant, splice_region_variant | 7/182 | 5 | NM_001164507.2 | A2 | |
NEB | ENST00000409198.5 | c.403G>C | p.Val135Leu | missense_variant, splice_region_variant | 7/150 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Cov.: 30
GnomAD4 genome ? Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at