chr19-4508916-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001367868.2(PLIN4):c.3554C>T(p.Ser1185Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000614 in 1,612,832 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001367868.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLIN4 | NM_001367868.2 | c.3554C>T | p.Ser1185Leu | missense_variant | 6/8 | ENST00000301286.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLIN4 | ENST00000301286.5 | c.3554C>T | p.Ser1185Leu | missense_variant | 6/8 | 5 | NM_001367868.2 | P1 | |
PLIN4 | ENST00000633942.1 | c.3557C>T | p.Ser1186Leu | missense_variant | 6/8 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000125 AC: 19AN: 152164Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000889 AC: 22AN: 247360Hom.: 0 AF XY: 0.0000817 AC XY: 11AN XY: 134694
GnomAD4 exome AF: 0.0000548 AC: 80AN: 1460550Hom.: 1 Cov.: 30 AF XY: 0.0000592 AC XY: 43AN XY: 726586
GnomAD4 genome ? AF: 0.000125 AC: 19AN: 152282Hom.: 0 Cov.: 32 AF XY: 0.000107 AC XY: 8AN XY: 74452
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 28, 2022 | The c.3512C>T (p.S1171L) alteration is located in exon 4 (coding exon 4) of the PLIN4 gene. This alteration results from a C to T substitution at nucleotide position 3512, causing the serine (S) at amino acid position 1171 to be replaced by a leucine (L). 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