rs892158

chr19-4507704-T-C

Variant summary

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

The NM_001367868.2(PLIN4):c.3702+1064A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.831 in 151,964 control chromosomes in the GnomAD database, including 52,663 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 0.83 (52663 hom., cov: 29)
• Consequence: PLIN4 NM_001367868.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95

Genes affected

PLIN4 (HGNC:29393): (perilipin 4) Members of the perilipin family, such as PLIN4, coat intracellular lipid storage droplets (Wolins et al., 2003 [PubMed 12840023]).[supplied by OMIM, Feb 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.88 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLIN4	NM_001367868.2	c.3702+1064A>G		intron_variant		ENST00000301286.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLIN4	ENST00000301286.5	c.3702+1064A>G		intron_variant		5	NM_001367868.2	P1
PLIN4	ENST00000633942.1	c.3705+1064A>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.831 AC: 126178 AN: 151846 Hom.: 52619 Cov.: 29

Gnomad AFR AF: 0.781

Gnomad AMI AF: 0.873

Gnomad AMR AF: 0.872

Gnomad ASJ AF: 0.825

Gnomad EAS AF: 0.902

Gnomad SAS AF: 0.705

Gnomad FIN AF: 0.873

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.849

Gnomad OTH AF: 0.825

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

GnomAD4 genome AF: 0.831 AC: 126275 AN: 151964 Hom.: 52663 Cov.: 29 AF XY: 0.832 AC XY: 61784 AN XY: 74286

Gnomad4 AFR AF: 0.781

Gnomad4 AMR AF: 0.872

Gnomad4 ASJ AF: 0.825

Gnomad4 EAS AF: 0.902

Gnomad4 SAS AF: 0.704

Gnomad4 FIN AF: 0.873

Gnomad4 NFE AF: 0.849

Gnomad4 OTH AF: 0.828

Alfa AF: 0.841 Hom.: 10265

Bravo AF: 0.832

Asia WGS AF: 0.802 AC: 2789 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.84
Dann	Benign	0.20

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: rs892158; hg19: chr19-4507716;