rs2437150
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_032018.7(SPRTN):c.887C>A(p.Pro296His) variant causes a missense 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. 14/21 in silico tools predict a benign outcome for this variant. 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. P296L) has been classified as Benign.
Frequency
Consequence
NM_032018.7 missense
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 |
---|---|---|---|---|---|---|---|
SPRTN | NM_032018.7 | c.887C>A | p.Pro296His | missense_variant | 5/5 | ENST00000295050.12 | |
SPRTN | XM_006711818.4 | c.758C>A | p.Pro253His | missense_variant | 4/4 | ||
SPRTN | NM_001010984.4 | c.*1172C>A | 3_prime_UTR_variant | 4/4 | |||
SPRTN | NM_001261462.3 | c.*1172C>A | 3_prime_UTR_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPRTN | ENST00000295050.12 | c.887C>A | p.Pro296His | missense_variant | 5/5 | 1 | NM_032018.7 | P1 | |
SPRTN | ENST00000391858.8 | c.*1172C>A | 3_prime_UTR_variant | 4/4 | 1 | ||||
SPRTN | ENST00000366644.3 | downstream_gene_variant | 5 | ||||||
SPRTN | ENST00000469904.1 | downstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Cov.: 58
GnomAD4 genome ? Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at