19-4504876-G-A
Variant summary
Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001367868.2(PLIN4):c.3774C>T(p.Asp1258Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000028 in 1,606,788 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 (★).
Frequency
Consequence
NM_001367868.2 synonymous
Scores
Clinical Significance
Conservation
Publications
- vacuolar NeuromyopathyInheritance: AD Classification: MODERATE Submitted by: Ambry Genetics
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ACMG classification
Our verdict: Benign. The variant received -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PLIN4 | NM_001367868.2 | c.3774C>T | p.Asp1258Asp | synonymous_variant | Exon 7 of 8 | ENST00000301286.5 | NP_001354797.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLIN4 | ENST00000301286.5 | c.3774C>T | p.Asp1258Asp | synonymous_variant | Exon 7 of 8 | 5 | NM_001367868.2 | ENSP00000301286.4 | ||
PLIN4 | ENST00000633942.1 | c.3777C>T | p.Asp1259Asp | synonymous_variant | Exon 7 of 8 | 5 | ENSP00000488481.1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152198Hom.: 0 Cov.: 33 show subpopulations
GnomAD2 exomes AF: 0.0000256 AC: 6AN: 234630 AF XY: 0.0000392 show subpopulations
GnomAD4 exome AF: 0.0000254 AC: 37AN: 1454472Hom.: 0 Cov.: 31 AF XY: 0.0000304 AC XY: 22AN XY: 722942 show subpopulations
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152316Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74482 show subpopulations
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at