1-99058491-A-G

Variant names:

• chr1-99058491-A-G
• rs10747502
• ENST00000696571.1:c.72+57100T>C

Variant summary

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

The ENST00000696571.1(PLPPR5):​c.72+57100T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.862 in 152,052 control chromosomes in the GnomAD database, including 57,228 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 0.86 (57228 hom., cov: 31)
• Consequence: PLPPR5 ENST00000696571.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 10 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLPPR5-AS1	NR_033940.1	n.370+53846A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLPPR5	ENST00000696571.1	c.72+57100T>C		intron_variant	Intron 2 of 6			ENSP00000512726.1
PLPPR5-AS1	ENST00000425113.1	n.370+53846A>G		intron_variant	Intron 1 of 2	2
PLPPR5-AS1	ENST00000647692.1	n.219+53846A>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.862 AC: 131028 AN: 151934 Hom.: 57194 Cov.: 31

Gnomad AFR AF: 0.718

Gnomad AMI AF: 0.910

Gnomad AMR AF: 0.919

Gnomad ASJ AF: 0.853

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.926

Gnomad FIN AF: 0.898

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.917

Gnomad OTH AF: 0.867

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

GnomAD4 genome AF: 0.862 AC: 131116 AN: 152052 Hom.: 57228 Cov.: 31 AF XY: 0.864 AC XY: 64199 AN XY: 74322

African (AFR) AF: 0.718 AC: 29782 AN: 41458

American (AMR) AF: 0.919 AC: 14039 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.853 AC: 2957 AN: 3468

East Asian (EAS) AF: 0.996 AC: 5149 AN: 5170

South Asian (SAS) AF: 0.926 AC: 4459 AN: 4816

European-Finnish (FIN) AF: 0.898 AC: 9509 AN: 10590

Middle Eastern (MID) AF: 0.884 AC: 260 AN: 294

European-Non Finnish (NFE) AF: 0.917 AC: 62305 AN: 67964

Other (OTH) AF: 0.869 AC: 1828 AN: 2104

Alfa AF: 0.897 Hom.: 197124

Bravo AF: 0.858

Asia WGS AF: 0.937 AC: 3252 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.20
DANN	Benign	0.49
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs10747502; hg19: chr1-99524047;