rs892157

Positions:

• chr19-4526170-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001013706.3(PLIN5):​c.521-338G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 152,094 control chromosomes in the GnomAD database, including 4,399 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.17 (4399 hom., cov: 31)
• Consequence: PLIN5 NM_001013706.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87

Genes affected

PLIN5 (HGNC:33196): (perilipin 5) Predicted to enable identical protein binding activity and lipase binding activity. Predicted to be involved in several processes, including negative regulation of peroxisome proliferator activated receptor signaling pathway; regulation of lipase activity; and regulation of lipid metabolic process. Located in intracellular membrane-bounded organelle and lipid droplet. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLIN5	NM_001013706.3	c.521-338G>C		intron_variant		ENST00000381848.7	NP_001013728.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLIN5	ENST00000381848.7	c.521-338G>C		intron_variant		1	NM_001013706.3	ENSP00000371272	P1

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26515 AN: 151976 Hom.: 4386 Cov.: 31

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0563

Gnomad FIN AF: 0.0494

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0761

Gnomad OTH AF: 0.148

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.175 AC: 26574 AN: 152094 Hom.: 4399 Cov.: 31 AF XY: 0.169 AC XY: 12561 AN XY: 74374

Gnomad4 AFR AF: 0.439

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0564

Gnomad4 FIN AF: 0.0494

Gnomad4 NFE AF: 0.0761

Gnomad4 OTH AF: 0.152

Alfa AF: 0.130 Hom.: 320

Bravo AF: 0.191

Asia WGS AF: 0.0590 AC: 205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.065
DANN	Benign	0.43

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.080		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs892157; hg19: chr19-4526182;