chr1-99058491-A-G

Position:

• chr1-99058491-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_033940.1(PLPPR5-AS1):​n.370+53846A>G 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 0.862 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-AS1 NR_033940.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24

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=-0.99).
• 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/exons	MANE	Protein	UniProt
PLPPR5-AS1	NR_033940.1	n.370+53846A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLPPR5-AS1	ENST00000658279.1	n.202+53846A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.718

Gnomad4 AMR AF: 0.919

Gnomad4 ASJ AF: 0.853

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.926

Gnomad4 FIN AF: 0.898

Gnomad4 NFE AF: 0.917

Gnomad4 OTH AF: 0.869

Alfa AF: 0.904 Hom.: 84434

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10747502; hg19: chr1-99524047;