10-26697780-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_014317.5(PDSS1):c.69C>T(p.Pro23=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000216 in 1,299,104 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. P23P) has been classified as Likely benign.
Frequency
Consequence
NM_014317.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDSS1 | NM_014317.5 | c.69C>T | p.Pro23= | synonymous_variant | 1/12 | ENST00000376215.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDSS1 | ENST00000376215.10 | c.69C>T | p.Pro23= | synonymous_variant | 1/12 | 1 | NM_014317.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 151926Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.0000218 AC: 25AN: 1147178Hom.: 0 Cov.: 30 AF XY: 0.0000307 AC XY: 17AN XY: 553744
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 151926Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74194
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 03, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at