11-824828-AGGCCCGGCCCGTGATCGG-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4
The NM_020376.4(PNPLA2):c.1487_1504delGGCCCGTGATCGGGGCCC(p.Arg496_Ala501del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000515 in 1,534,660 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_020376.4 disruptive_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PNPLA2 | ENST00000336615.9 | c.1487_1504delGGCCCGTGATCGGGGCCC | p.Arg496_Ala501del | disruptive_inframe_deletion | Exon 10 of 10 | 1 | NM_020376.4 | ENSP00000337701.4 | ||
PNPLA2 | ENST00000529255.1 | n.917_934delGGCCCGTGATCGGGGCCC | non_coding_transcript_exon_variant | Exon 4 of 4 | 1 | |||||
PNPLA2 | ENST00000525250.5 | n.2341_2358delGGCCCGTGATCGGGGCCC | non_coding_transcript_exon_variant | Exon 6 of 6 | 2 | |||||
ENSG00000255108 | ENST00000532946.1 | n.307-983_307-966delCCGATCACGGGCCGGGCC | intron_variant | Intron 2 of 2 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152100Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000541 AC: 7AN: 129428Hom.: 0 AF XY: 0.0000283 AC XY: 2AN XY: 70712
GnomAD4 exome AF: 0.0000506 AC: 70AN: 1382560Hom.: 0 AF XY: 0.0000542 AC XY: 37AN XY: 682358
GnomAD4 genome AF: 0.0000592 AC: 9AN: 152100Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74306
ClinVar
Submissions by phenotype
Neutral lipid storage myopathy Uncertain:1
This variant, c.1487_1504del, results in the deletion of 6 amino acid(s) of the PNPLA2 protein (p.Arg496_Ala501del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs747915336, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with PNPLA2-related conditions. ClinVar contains an entry for this variant (Variation ID: 465787). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
See cases Uncertain:1
ACMG classification criteria: PM2, PM4 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at