22-21703882-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_013313.5(YPEL1):c.118T>C(p.Ser40Pro) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_013313.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
YPEL1 | NM_013313.5 | c.118T>C | p.Ser40Pro | missense_variant, splice_region_variant | 3/5 | ENST00000339468.8 | |
YPEL1 | XM_047441355.1 | c.118T>C | p.Ser40Pro | missense_variant, splice_region_variant | 3/5 | ||
YPEL1 | XM_047441356.1 | c.118T>C | p.Ser40Pro | missense_variant, splice_region_variant | 3/5 | ||
YPEL1 | NR_130910.2 | n.846T>C | non_coding_transcript_exon_variant | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
YPEL1 | ENST00000339468.8 | c.118T>C | p.Ser40Pro | missense_variant, splice_region_variant | 3/5 | 1 | NM_013313.5 | P1 | |
YPEL1 | ENST00000672036.2 | c.223T>C | p.Ser75Pro | missense_variant, splice_region_variant | 2/4 | ||||
YPEL1 | ENST00000477675.1 | n.813T>C | non_coding_transcript_exon_variant | 3/5 | 2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Cov.: 33
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.