chr19-4506903-A-G

Position:

• chr19-4506903-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.3702+1865T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0967 in 152,304 control chromosomes in the GnomAD database, including 894 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 0.097 (894 hom., cov: 33)
• Consequence: PLIN4 NM_001367868.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.562

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=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLIN4	NM_001367868.2	c.3702+1865T>C		intron_variant		ENST00000301286.5	NP_001354797.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLIN4	ENST00000301286.5	c.3702+1865T>C		intron_variant		5	NM_001367868.2	ENSP00000301286.4
PLIN4	ENST00000633942.1	c.3705+1865T>C		intron_variant		5		ENSP00000488481.1

Frequencies

GnomAD3 genomes AF: 0.0968 AC: 14729 AN: 152186 Hom.: 893 Cov.: 33

Gnomad AFR AF: 0.0416

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.0891

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.0805

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.0967 AC: 14729 AN: 152304 Hom.: 894 Cov.: 33 AF XY: 0.0981 AC XY: 7303 AN XY: 74472

Gnomad4 AFR AF: 0.0416

Gnomad4 AMR AF: 0.0889

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.0805

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.108

Gnomad4 NFE AF: 0.119

Gnomad4 OTH AF: 0.121

Alfa AF: 0.114 Hom.: 920

Bravo AF: 0.0921

Asia WGS AF: 0.149 AC: 519 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.90
DANN	Benign	0.53

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: rs11673616; hg19: chr19-4506915;