chr2-55636315-G-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_033109.5(PNPT1):c.2274C>A(p.Thr758=) variant causes a synonymous 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. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. T758T) has been classified as Likely benign.
Frequency
Consequence
NM_033109.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PNPT1 | NM_033109.5 | c.2274C>A | p.Thr758= | synonymous_variant | 28/28 | ENST00000447944.7 | |
PNPT1 | XM_005264629.3 | c.2034C>A | p.Thr678= | synonymous_variant | 28/28 | ||
PNPT1 | XM_017005172.2 | c.2034C>A | p.Thr678= | synonymous_variant | 27/27 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PNPT1 | ENST00000447944.7 | c.2274C>A | p.Thr758= | synonymous_variant | 28/28 | 1 | NM_033109.5 | P1 | |
PNPT1 | ENST00000415374.5 | c.2274C>A | p.Thr758= | synonymous_variant, NMD_transcript_variant | 28/29 | 5 | |||
PNPT1 | ENST00000260604.8 | c.*1816C>A | 3_prime_UTR_variant, NMD_transcript_variant | 27/27 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome Cov.: 32
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 13, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.