chr22-46235130-T-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_005036.6(PPARA):c.1160-3T>C variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000589 in 1,614,020 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/2 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_005036.6 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPARA | NM_005036.6 | c.1160-3T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000407236.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPARA | ENST00000407236.6 | c.1160-3T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_005036.6 | P1 | |||
PPARA | ENST00000402126.1 | c.1160-3T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000854 AC: 13AN: 152224Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000299 AC: 75AN: 250602Hom.: 0 AF XY: 0.000288 AC XY: 39AN XY: 135504
GnomAD4 exome AF: 0.0000561 AC: 82AN: 1461678Hom.: 1 Cov.: 31 AF XY: 0.0000536 AC XY: 39AN XY: 727144
GnomAD4 genome ? AF: 0.0000853 AC: 13AN: 152342Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74494
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | May 30, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at