rs12979855

Variant names:

• chr19-4851096-G-T
• rs12979855
• NM_005817.5:c.634+920C>A

Variant summary

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

The NM_005817.5(PLIN3):​c.634+920C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.607 in 151,864 control chromosomes in the GnomAD database, including 28,190 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 0.61 (28190 hom., cov: 32)
• Consequence: PLIN3 NM_005817.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.34
• Publications: 1 publications found

Genes affected

PLIN3 (HGNC:16893): (perilipin 3) Mannose 6-phophate receptors (MPRs) deliver lysosomal hydrolase from the Golgi to endosomes and then return to the Golgi complex. The protein encoded by this gene interacts with the cytoplasmic domains of both cation-independent and cation-dependent MPRs, and is required for endosome-to-Golgi transport. This protein also binds directly to the GTPase RAB9 (RAB9A), a member of the RAS oncogene family. The interaction with RAB9 has been shown to increase the affinity of this protein for its cargo. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Aug 2009]

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 (SAS) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005817.5. 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
	PLIN3	NM_005817.5	MANE Select	c.634+920C>A		intron	N/A	NP_005808.3
	PLIN3	NM_001164189.2		c.634+920C>A		intron	N/A	NP_001157661.1	O60664-3
	PLIN3	NM_001164194.2		c.598+920C>A		intron	N/A	NP_001157666.1	O60664-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLIN3	ENST00000221957.9	TSL:1 MANE Select	c.634+920C>A		intron	N/A	ENSP00000221957.3	O60664-1
	PLIN3	ENST00000585479.5	TSL:1	c.634+920C>A		intron	N/A	ENSP00000465596.1	O60664-3
	PLIN3	ENST00000884464.1		c.634+920C>A		intron	N/A	ENSP00000554523.1

Frequencies

GnomAD3 genomes AF: 0.607 AC: 92084 AN: 151746 Hom.: 28196 Cov.: 32

Gnomad AFR AF: 0.613

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.547

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.649

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.612

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

GnomAD4 genome AF: 0.607 AC: 92110 AN: 151864 Hom.: 28190 Cov.: 32 AF XY: 0.598 AC XY: 44354 AN XY: 74220

African (AFR) AF: 0.613 AC: 25382 AN: 41418

American (AMR) AF: 0.613 AC: 9308 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.547 AC: 1900 AN: 3472

East Asian (EAS) AF: 0.442 AC: 2280 AN: 5162

South Asian (SAS) AF: 0.648 AC: 3122 AN: 4816

European-Finnish (FIN) AF: 0.458 AC: 4818 AN: 10518

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.637 AC: 43329 AN: 67968

Other (OTH) AF: 0.604 AC: 1276 AN: 2114

Alfa AF: 0.617 Hom.: 3623

Bravo AF: 0.620

Asia WGS AF: 0.516 AC: 1796 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	0.42
DANN	Benign	0.76
PhyloP100		-3.3
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: rs12979855; hg19: chr19-4851108;