chr19-4516970-A-G

Variant names:

• chr19-4516970-A-G
• rs8102428
• NM_001367868.2:c.197-292T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001367868.2(PLIN4):​c.197-292T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 152,144 control chromosomes in the GnomAD database, including 6,156 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 0.21 (6156 hom., cov: 33)
• Consequence: PLIN4 NM_001367868.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 7 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.509 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.197-292T>C		intron	N/A	NP_001354797.1	Q96Q06
	PLIN4	NM_001393888.1		c.197-292T>C		intron	N/A	NP_001380817.1	A0A0J9YXN7
	PLIN4	NM_001393889.1		c.197-292T>C		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.197-292T>C		intron	N/A	ENSP00000301286.4	Q96Q06
	PLIN4	ENST00000966625.1		c.197-292T>C		intron	N/A	ENSP00000636684.1
	PLIN4	ENST00000966622.1		c.197-292T>C		intron	N/A	ENSP00000636681.1

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31398 AN: 152026 Hom.: 6133 Cov.: 33

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0364

Gnomad FIN AF: 0.0513

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0965

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.207 AC: 31474 AN: 152144 Hom.: 6156 Cov.: 33 AF XY: 0.198 AC XY: 14750 AN XY: 74400

African (AFR) AF: 0.515 AC: 21373 AN: 41488

American (AMR) AF: 0.124 AC: 1890 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 465 AN: 3472

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5170

South Asian (SAS) AF: 0.0358 AC: 173 AN: 4826

European-Finnish (FIN) AF: 0.0513 AC: 544 AN: 10612

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0966 AC: 6563 AN: 67968

Other (OTH) AF: 0.169 AC: 356 AN: 2110

Alfa AF: 0.145 Hom.: 994

Bravo AF: 0.226

Asia WGS AF: 0.0580 AC: 201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.11
DANN	Benign	0.21
PhyloP100		-1.3
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs8102428; hg19: chr19-4516982;