chr2-160057182-A-G

Position:

• chr2-160057182-A-G

Variant summary

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

The NM_007366.5(PLA2R1):​c.109+5113T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.79 in 152,136 control chromosomes in the GnomAD database, including 48,432 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 0.79 (48432 hom., cov: 31)
• Consequence: PLA2R1 NM_007366.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.188

Genes affected

PLA2R1 (HGNC:9042): (phospholipase A2 receptor 1) This gene represents a phospholipase A2 receptor. The encoded protein likely exists as both a transmembrane form and a soluble form. The transmembrane receptor may play a role in clearance of phospholipase A2, thereby inhibiting its action. Polymorphisms at this locus have been associated with susceptibility to idiopathic membranous nephropathy. Alternatively spliced transcript variants encoding different isoforms have been identified.[provided by RefSeq, Sep 2010]

LOC105373717 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLA2R1	NM_007366.5	c.109+5113T>C		intron_variant		ENST00000283243.13
LOC105373717	XR_007087274.1	n.221+952A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLA2R1	ENST00000283243.13	c.109+5113T>C		intron_variant		1	NM_007366.5	P1
PLA2R1	ENST00000392771.1	c.109+5113T>C		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.790 AC: 120084 AN: 152018 Hom.: 48373 Cov.: 31

Gnomad AFR AF: 0.945

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.812

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.636

Gnomad FIN AF: 0.750

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.726

Gnomad OTH AF: 0.738

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

GnomAD4 genome AF: 0.790 AC: 120207 AN: 152136 Hom.: 48432 Cov.: 31 AF XY: 0.791 AC XY: 58772 AN XY: 74340

Gnomad4 AFR AF: 0.946

Gnomad4 AMR AF: 0.812

Gnomad4 ASJ AF: 0.603

Gnomad4 EAS AF: 0.744

Gnomad4 SAS AF: 0.636

Gnomad4 FIN AF: 0.750

Gnomad4 NFE AF: 0.726

Gnomad4 OTH AF: 0.739

Alfa AF: 0.735 Hom.: 20728

Bravo AF: 0.806

Asia WGS AF: 0.722 AC: 2513 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.6
DANN	Benign	0.79

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2667033; hg19: chr2-160913693;