chr6-36291464-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 5P and 1B. PM1PM2PP5BP4
The NM_001374623.1(PNPLA1):c.350C>T(p.Thr117Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000118 in 1,613,508 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (no stars).
Frequency
Consequence
NM_001374623.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PNPLA1 | NM_001374623.1 | c.350C>T | p.Thr117Met | missense_variant | 2/9 | ENST00000636260.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PNPLA1 | ENST00000636260.2 | c.350C>T | p.Thr117Met | missense_variant | 2/9 | 5 | NM_001374623.1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 151636Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251452Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135902
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461872Hom.: 0 Cov.: 32 AF XY: 0.0000165 AC XY: 12AN XY: 727240
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 151636Hom.: 0 Cov.: 31 AF XY: 0.0000270 AC XY: 2AN XY: 73988
ClinVar
Submissions by phenotype
Autosomal recessive congenital ichthyosis 10 Pathogenic:1
Likely pathogenic, no assertion criteria provided | provider interpretation;research | Unité de Différenciation Epithéliale et Auto-Immunité Rhumatoïde, INSERM - Université Paul Sabatier | - | This variant has been seen as a compound heterozygote in association with c.[335C>A], [p.Ser112Tyr]. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at