chr1-40092125-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):āc.282A>Gā(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 (ā ). 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
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Apr 10, 2021 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 06, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at