rs160016

chr1-99120836-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NR_033940.1(PLPPR5-AS1):n.371-23200C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0378 in 152,200 control chromosomes in the GnomAD database, including 122 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 (122 hom., cov: 32)
• Consequence: PLPPR5-AS1 NR_033940.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.26

Genes affected

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

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0378 (5757/152200) while in subpopulation NFE AF= 0.0501 (3409/68008). AF 95% confidence interval is 0.0487. There are 122 homozygotes in gnomad4. There are 2741 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 123 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLPPR5-AS1	NR_033940.1	n.371-23200C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLPPR5-AS1	ENST00000658279.1	n.203-81093C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0378 AC: 5754 AN: 152084 Hom.: 123 Cov.: 32

Gnomad AFR AF: 0.0238

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0352

Gnomad ASJ AF: 0.0487

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0493

Gnomad FIN AF: 0.0264

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0501

Gnomad OTH AF: 0.0484

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

GnomAD4 genome AF: 0.0378 AC: 5757 AN: 152200 Hom.: 122 Cov.: 32 AF XY: 0.0368 AC XY: 2741 AN XY: 74388

Gnomad4 AFR AF: 0.0239

Gnomad4 AMR AF: 0.0351

Gnomad4 ASJ AF: 0.0487

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.0490

Gnomad4 FIN AF: 0.0264

Gnomad4 NFE AF: 0.0501

Gnomad4 OTH AF: 0.0479

Alfa AF: 0.0440 Hom.: 41

Bravo AF: 0.0370

Asia WGS AF: 0.0250 AC: 88 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.12
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs160016; hg19: chr1-99586392;