1-40092125-T-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_000310.4(PPT1):c.282A>G(p.Thr94=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000109 in 1,461,770 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. T94T) has been classified as Likely benign.
Frequency
Consequence
NM_000310.4 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 |
---|---|---|---|---|---|---|---|
PPT1 | NM_000310.4 | c.282A>G | p.Thr94= | synonymous_variant | 3/9 | ENST00000642050.2 | |
PPT1 | NM_001363695.2 | c.282A>G | p.Thr94= | synonymous_variant | 3/8 | ||
PPT1 | NM_001142604.2 | c.125-2613A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPT1 | ENST00000642050.2 | c.282A>G | p.Thr94= | synonymous_variant | 3/9 | NM_000310.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.0000278 AC: 7AN: 251474Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135908
GnomAD4 exome AF: 0.0000109 AC: 16AN: 1461770Hom.: 0 Cov.: 33 AF XY: 0.0000138 AC XY: 10AN XY: 727198
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Neuronal ceroid lipofuscinosis 1 Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 06, 2023 | - - |
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Apr 10, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at