chr19-4839305-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005817.5(PLIN3):c.1192C>T(p.Arg398Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000694 in 1,614,000 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R398L) has been classified as Uncertain significance.
Frequency
Consequence
NM_005817.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLIN3 | NM_005817.5 | c.1192C>T | p.Arg398Cys | missense_variant | 8/8 | ENST00000221957.9 | |
PLIN3 | NM_001164189.2 | c.1189C>T | p.Arg397Cys | missense_variant | 8/8 | ||
PLIN3 | NM_001164194.2 | c.1156C>T | p.Arg386Cys | missense_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLIN3 | ENST00000221957.9 | c.1192C>T | p.Arg398Cys | missense_variant | 8/8 | 1 | NM_005817.5 | P3 | |
PLIN3 | ENST00000585479.5 | c.1189C>T | p.Arg397Cys | missense_variant | 8/8 | 1 | A1 | ||
PLIN3 | ENST00000592528.5 | c.1156C>T | p.Arg386Cys | missense_variant | 8/8 | 2 | |||
PLIN3 | ENST00000589163.5 | c.766C>T | p.Arg256Cys | missense_variant | 5/5 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152096Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000152 AC: 38AN: 250720Hom.: 1 AF XY: 0.000199 AC XY: 27AN XY: 135586
GnomAD4 exome AF: 0.0000725 AC: 106AN: 1461786Hom.: 1 Cov.: 31 AF XY: 0.0000921 AC XY: 67AN XY: 727174
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152214Hom.: 0 Cov.: 31 AF XY: 0.0000672 AC XY: 5AN XY: 74428
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 30, 2023 | The c.1192C>T (p.R398C) alteration is located in exon 8 (coding exon 7) of the PLIN3 gene. This alteration results from a C to T substitution at nucleotide position 1192, causing the arginine (R) at amino acid position 398 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at