8-26581971-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PP2PP5_Moderate
The NM_001197293.3(DPYSL2):c.357C>A(p.Ser119Arg) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. S119S) has been classified as Benign.
Frequency
Consequence
NM_001197293.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DPYSL2 | NM_001197293.3 | c.357C>A | p.Ser119Arg | missense_variant, splice_region_variant | 2/14 | ENST00000521913.7 | |
DPYSL2 | NM_001386.6 | c.42C>A | p.Ser14Arg | missense_variant, splice_region_variant | 2/14 | ||
DPYSL2 | NM_001244604.2 | c.-67C>A | splice_region_variant, 5_prime_UTR_variant | 2/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DPYSL2 | ENST00000521913.7 | c.357C>A | p.Ser119Arg | missense_variant, splice_region_variant | 2/14 | 1 | NM_001197293.3 | ||
DPYSL2 | ENST00000311151.9 | c.42C>A | p.Ser14Arg | missense_variant, splice_region_variant | 2/14 | 1 | P1 | ||
DPYSL2 | ENST00000493789.6 | c.258C>A | p.Ser86Arg | missense_variant, splice_region_variant | 2/3 | 4 | |||
DPYSL2 | ENST00000523027.1 | c.-67C>A | splice_region_variant, 5_prime_UTR_variant | 2/14 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Cov.: 30
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Inborn genetic diseases Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 18, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at