chr10-13319210-G-C
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 7P and 1B. PM2PM5PP2PP5_ModerateBP4
The NM_012247.5(SEPHS1):c.1111C>G(p.Arg371Gly) variant causes a missense change involving the alteration of a 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 pathogenic (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R371Q) has been classified as Pathogenic.
Frequency
Consequence
NM_012247.5 missense
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 |
---|---|---|---|---|---|---|---|
SEPHS1 | NM_012247.5 | c.1111C>G | p.Arg371Gly | missense_variant | 9/9 | ENST00000327347.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEPHS1 | ENST00000327347.10 | c.1111C>G | p.Arg371Gly | missense_variant | 9/9 | 1 | NM_012247.5 | P1 | |
SEPHS1 | ENST00000545675.5 | c.910C>G | p.Arg304Gly | missense_variant | 8/8 | 1 | |||
SEPHS1 | ENST00000378614.8 | c.898C>G | p.Arg300Gly | missense_variant | 8/8 | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome Cov.: 31
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not provided Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Jun 30, 2022 | Not observed in large population cohorts (gnomAD); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Has not been previously published as pathogenic or benign to our knowledge - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.