rs11670485

chr19-4525205-G-A

Variant summary

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

The NM_001013706.3(PLIN5):c.721-129C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0562 in 606,712 control chromosomes in the GnomAD database, including 1,206 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 0.050 (268 hom., cov: 31)
  • Exomes 𝑓: 0.058 (938 hom.)
• Consequence: PLIN5 NM_001013706.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.58

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=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0714 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLIN5	NM_001013706.3	c.721-129C>T		intron_variant		ENST00000381848.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLIN5	ENST00000381848.7	c.721-129C>T		intron_variant		1	NM_001013706.3	P1
PLIN5	ENST00000589728.1	n.218-129C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0502 AC: 7643 AN: 152148 Hom.: 268 Cov.: 31

Gnomad AFR AF: 0.0134

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.0532

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.0419

Gnomad FIN AF: 0.0489

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0731

Gnomad OTH AF: 0.0594

GnomAD4 exome AF: 0.0582 AC: 26469 AN: 454446 Hom.: 938 AF XY: 0.0579 AC XY: 13572 AN XY: 234576

Gnomad4 AFR exome AF: 0.0112

Gnomad4 AMR exome AF: 0.0461

Gnomad4 ASJ exome AF: 0.111

Gnomad4 EAS exome AF: 0.000186

Gnomad4 SAS exome AF: 0.0391

Gnomad4 FIN exome AF: 0.0451

Gnomad4 NFE exome AF: 0.0674

Gnomad4 OTH exome AF: 0.0604

GnomAD4 genome AF: 0.0502 AC: 7639 AN: 152266 Hom.: 268 Cov.: 31 AF XY: 0.0486 AC XY: 3615 AN XY: 74448

Gnomad4 AFR AF: 0.0134

Gnomad4 AMR AF: 0.0531

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.000385

Gnomad4 SAS AF: 0.0415

Gnomad4 FIN AF: 0.0489

Gnomad4 NFE AF: 0.0731

Gnomad4 OTH AF: 0.0588

Alfa AF: 0.0591 Hom.: 42

Bravo AF: 0.0495

Asia WGS AF: 0.0200 AC: 71 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.17
Dann	Benign	0.41

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs11670485; hg19: chr19-4525217;