rs892158

Variant names:

• chr19-4507704-T-C
• rs892158
• NM_001367868.2:c.3702+1064A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

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]

PLIN4 Gene-Disease associations (from GenCC):

• vacuolar Neuromyopathy

  Inheritance: AD Classification: MODERATE Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001367868.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLIN4	NM_001367868.2	MANE Select	c.3702+1064A>G		intron	N/A	NP_001354797.1	Q96Q06
	PLIN4	NM_001393888.1		c.3705+1064A>G		intron	N/A	NP_001380817.1	A0A0J9YXN7
	PLIN4	NM_001393889.1		c.3705+1064A>G		intron	N/A	NP_001380818.1	A0A0J9YXN7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLIN4	ENST00000301286.5	TSL:5 MANE Select	c.3702+1064A>G		intron	N/A	ENSP00000301286.4	Q96Q06
	PLIN4	ENST00000966625.1		c.3888+1064A>G		intron	N/A	ENSP00000636684.1
	PLIN4	ENST00000966622.1		c.3885+1064A>G		intron	N/A	ENSP00000636681.1

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

African (AFR) AF: 0.781 AC: 32341 AN: 41398

American (AMR) AF: 0.872 AC: 13312 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.825 AC: 2865 AN: 3472

East Asian (EAS) AF: 0.902 AC: 4643 AN: 5150

South Asian (SAS) AF: 0.704 AC: 3392 AN: 4816

European-Finnish (FIN) AF: 0.873 AC: 9243 AN: 10586

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.849 AC: 57712 AN: 67964

Other (OTH) AF: 0.828 AC: 1745 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.84
DANN	Benign	0.20
PhyloP100		-2.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs892158; hg19: chr19-4507716;