19-4516970-A-G

Position:

• chr19-4516970-A-G

Variant summary

Our verdict is Benign. Variant got -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

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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.509 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLIN4	NM_001367868.2	c.197-292T>C		intron_variant		ENST00000301286.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLIN4	ENST00000301286.5	c.197-292T>C		intron_variant		5	NM_001367868.2	P1
PLIN4	ENST00000633942.1	c.197-292T>C		intron_variant		5

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

Gnomad4 AFR AF: 0.515

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0358

Gnomad4 FIN AF: 0.0513

Gnomad4 NFE AF: 0.0966

Gnomad4 OTH AF: 0.169

Alfa AF: 0.140 Hom.: 783

Bravo AF: 0.226

Asia WGS AF: 0.0580 AC: 201 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	0.11
DANN	Benign	0.21

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

Publications

LitVar

Other links and lift over

dbSNP: rs8102428; hg19: chr19-4516982;