1-99119748-G-C

Variant names:

• chr1-99119748-G-C
• rs302739
• ENST00000696571.1:c.-6-4080C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000696571.1(PLPPR5):​c.-6-4080C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0378 in 152,172 control chromosomes in the GnomAD database, including 121 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 0.038 (121 hom., cov: 32)
• Consequence: PLPPR5 ENST00000696571.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0690
• Publications: 3 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=-0.92).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0378 (5749/152172) while in subpopulation NFE AF = 0.0501 (3408/67998). AF 95% confidence interval is 0.0487. There are 121 homozygotes in GnomAd4. There are 2741 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 121 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000696571.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLPPR5-AS1	NR_033940.1		n.371-24288G>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLPPR5	ENST00000696571.1		c.-6-4080C>G		intron	N/A	ENSP00000512726.1
	PLPPR5-AS1	ENST00000425113.1	TSL:2	n.371-24288G>C		intron	N/A
	PLPPR5-AS1	ENST00000647692.1		n.220-24288G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0378 AC: 5745 AN: 152054 Hom.: 122 Cov.: 32

Gnomad AFR AF: 0.0236

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0351

Gnomad ASJ AF: 0.0484

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0499

Gnomad FIN AF: 0.0264

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0501

Gnomad OTH AF: 0.0482

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

GnomAD4 genome AF: 0.0378 AC: 5749 AN: 152172 Hom.: 121 Cov.: 32 AF XY: 0.0368 AC XY: 2741 AN XY: 74406

African (AFR) AF: 0.0237 AC: 986 AN: 41516

American (AMR) AF: 0.0350 AC: 534 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0484 AC: 168 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5168

South Asian (SAS) AF: 0.0497 AC: 240 AN: 4828

European-Finnish (FIN) AF: 0.0264 AC: 280 AN: 10610

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0501 AC: 3408 AN: 67998

Other (OTH) AF: 0.0477 AC: 101 AN: 2116

Alfa AF: 0.00770 Hom.: 3

Bravo AF: 0.0370

Asia WGS AF: 0.0260 AC: 89 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.60
PhyloP100		-0.069

Splicing

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

Other links and lift over

dbSNP: rs302739; hg19: chr1-99585304;