1-99123823-C-T

Variant names:

• chr1-99123823-C-T
• rs303386
• ENST00000696571.1:c.-6-8155G>A

Variant summary

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

The ENST00000696571.1(PLPPR5):​c.-6-8155G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.658 in 151,894 control chromosomes in the GnomAD database, including 33,279 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 0.66 (33279 hom., cov: 31)
• Consequence: PLPPR5 ENST00000696571.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42
• Publications: 5 publications found

Genes affected

PLPPR5 (HGNC:31703): (phospholipid phosphatase related 5) The protein encoded by this gene is a type 2 member of the phosphatidic acid phosphatase (PAP) family. All type 2 members of this protein family contain 6 transmembrane regions, and a consensus N-glycosylation site. PAPs convert phosphatidic acid to diacylglycerol, and function in de novo synthesis of glycerolipids as well as in receptor-activated signal transduction mediated by phospholipase D. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]

PLPPR5-AS1 (HGNC:55720): (PLPPR5 antisense RNA 1)

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 (SAS) allele frequency at 95% confidence interval = 0.729 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLPPR5-AS1	NR_033940.1	n.371-20213C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLPPR5	ENST00000696571.1	c.-6-8155G>A		intron_variant	Intron 1 of 6			ENSP00000512726.1
PLPPR5-AS1	ENST00000425113.1	n.371-20213C>T		intron_variant	Intron 1 of 2	2
PLPPR5-AS1	ENST00000647692.1	n.220-20213C>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.658 AC: 99902 AN: 151776 Hom.: 33248 Cov.: 31

Gnomad AFR AF: 0.590

Gnomad AMI AF: 0.798

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.487

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.619

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.668

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

GnomAD4 genome AF: 0.658 AC: 99993 AN: 151894 Hom.: 33279 Cov.: 31 AF XY: 0.654 AC XY: 48572 AN XY: 74222

African (AFR) AF: 0.591 AC: 24437 AN: 41370

American (AMR) AF: 0.635 AC: 9687 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.709 AC: 2463 AN: 3472

East Asian (EAS) AF: 0.488 AC: 2510 AN: 5146

South Asian (SAS) AF: 0.749 AC: 3601 AN: 4808

European-Finnish (FIN) AF: 0.619 AC: 6522 AN: 10542

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.712 AC: 48415 AN: 67978

Other (OTH) AF: 0.668 AC: 1409 AN: 2110

Alfa AF: 0.692 Hom.: 120571

Bravo AF: 0.654

Asia WGS AF: 0.590 AC: 2049 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.10
DANN	Benign	0.48
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs303386; hg19: chr1-99589379;