rs1609717

Variant names:

• chr19-4519438-G-A
• rs1609717
• ENST00000966619.1:c.-1166C>T

Your query was ambiguous. Multiple possible variants found:

• chr19-4519438-G-A
• chr19-4519438-G-C

Variant summary

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

The ENST00000966619.1(PLIN4):​c.-1166C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.951 in 152,208 control chromosomes in the GnomAD database, including 68,927 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 0.95 (68927 hom., cov: 33)
• Consequence: PLIN4 ENST00000966619.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.953 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000966619.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLIN4	ENST00000966619.1		c.-1166C>T		5_prime_UTR	Exon 1 of 7	ENSP00000636678.1

Frequencies

GnomAD3 genomes AF: 0.951 AC: 144713 AN: 152090 Hom.: 68878 Cov.: 33

Gnomad AFR AF: 0.958

Gnomad AMI AF: 0.985

Gnomad AMR AF: 0.962

Gnomad ASJ AF: 0.952

Gnomad EAS AF: 0.976

Gnomad SAS AF: 0.901

Gnomad FIN AF: 0.945

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.947

Gnomad OTH AF: 0.953

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

GnomAD4 genome AF: 0.951 AC: 144820 AN: 152208 Hom.: 68927 Cov.: 33 AF XY: 0.950 AC XY: 70738 AN XY: 74426

African (AFR) AF: 0.958 AC: 39804 AN: 41560

American (AMR) AF: 0.962 AC: 14716 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.952 AC: 3307 AN: 3472

East Asian (EAS) AF: 0.976 AC: 5016 AN: 5140

South Asian (SAS) AF: 0.900 AC: 4344 AN: 4824

European-Finnish (FIN) AF: 0.945 AC: 10029 AN: 10618

Middle Eastern (MID) AF: 0.946 AC: 278 AN: 294

European-Non Finnish (NFE) AF: 0.947 AC: 64412 AN: 67982

Other (OTH) AF: 0.954 AC: 2016 AN: 2114

Alfa AF: 0.951 Hom.: 93816

Bravo AF: 0.956

Asia WGS AF: 0.943 AC: 3280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.039
DANN	Benign	0.53
PhyloP100		-2.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1609717; hg19: chr19-4519450;