chr15-89668913-T-C

Position:

• chr15-89668913-T-C

Variant summary

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

The ENST00000300055.10(PLIN1):​c.771+587A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.582 in 152,144 control chromosomes in the GnomAD database, including 27,296 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 0.58 (27296 hom., cov: 32)
• Consequence: PLIN1 ENST00000300055.10 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.239

Genes affected

PLIN1 (HGNC:9076): (perilipin 1) The protein encoded by this gene coats lipid storage droplets in adipocytes, thereby protecting them until they can be broken down by hormone-sensitive lipase. The encoded protein is the major cAMP-dependent protein kinase substrate in adipocytes and, when unphosphorylated, may play a role in the inhibition of lipolysis. Alternatively spliced transcript variants varying in the 5' UTR, but encoding the same protein, have been found for this gene. [provided by RefSeq, Feb 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.702 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLIN1	NM_002666.5	c.771+587A>G		intron_variant		ENST00000300055.10	NP_002657.3
PLIN1	NM_001145311.2	c.771+587A>G		intron_variant			NP_001138783.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLIN1	ENST00000300055.10	c.771+587A>G		intron_variant		1	NM_002666.5	ENSP00000300055	P1
PLIN1	ENST00000430628.2	c.771+587A>G		intron_variant		5		ENSP00000402167	P1

Frequencies

GnomAD3 genomes AF: 0.582 AC: 88550 AN: 152026 Hom.: 27292 Cov.: 32

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.866

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.663

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.707

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.582 AC: 88590 AN: 152144 Hom.: 27296 Cov.: 32 AF XY: 0.580 AC XY: 43110 AN XY: 74376

Gnomad4 AFR AF: 0.389

Gnomad4 AMR AF: 0.546

Gnomad4 ASJ AF: 0.612

Gnomad4 EAS AF: 0.356

Gnomad4 SAS AF: 0.574

Gnomad4 FIN AF: 0.663

Gnomad4 NFE AF: 0.707

Gnomad4 OTH AF: 0.605

Alfa AF: 0.675 Hom.: 48124

Bravo AF: 0.560

Asia WGS AF: 0.449 AC: 1564 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.8
DANN	Benign	0.82

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: rs8179043; hg19: chr15-90212144;