chr2-159994004-C-A

Variant names:

• chr2-159994004-C-A
• rs1606116
• NM_007366.5:c.1835-6646G>T

Variant summary

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

The NM_007366.5(PLA2R1):​c.1835-6646G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.059 in 151,834 control chromosomes in the GnomAD database, including 470 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 0.059 (470 hom., cov: 31)
• Consequence: PLA2R1 NM_007366.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 1 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007366.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLA2R1	NM_007366.5	MANE Select	c.1835-6646G>T		intron	N/A	NP_031392.3
	PLA2R1	NM_001195641.2		c.1835-6646G>T		intron	N/A	NP_001182570.1	B7ZML4
	PLA2R1	NM_001007267.3		c.1835-6646G>T		intron	N/A	NP_001007268.1	Q13018-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLA2R1	ENST00000283243.13	TSL:1 MANE Select	c.1835-6646G>T		intron	N/A	ENSP00000283243.7	Q13018-1
	PLA2R1	ENST00000392771.1	TSL:1	c.1835-6646G>T		intron	N/A	ENSP00000376524.1	Q13018-2
	PLA2R1	ENST00000890090.1		c.1835-6646G>T		intron	N/A	ENSP00000560149.1

Frequencies

GnomAD3 genomes AF: 0.0590 AC: 8949 AN: 151716 Hom.: 472 Cov.: 31

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0452

Gnomad ASJ AF: 0.0415

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.0857

Gnomad FIN AF: 0.0114

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0190

Gnomad OTH AF: 0.0384

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

GnomAD4 genome AF: 0.0590 AC: 8960 AN: 151834 Hom.: 470 Cov.: 31 AF XY: 0.0595 AC XY: 4421 AN XY: 74262

African (AFR) AF: 0.128 AC: 5284 AN: 41356

American (AMR) AF: 0.0452 AC: 688 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.0415 AC: 144 AN: 3472

East Asian (EAS) AF: 0.181 AC: 933 AN: 5160

South Asian (SAS) AF: 0.0853 AC: 412 AN: 4828

European-Finnish (FIN) AF: 0.0114 AC: 120 AN: 10558

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0190 AC: 1288 AN: 67908

Other (OTH) AF: 0.0408 AC: 86 AN: 2108

Alfa AF: 0.0432 Hom.: 100

Bravo AF: 0.0639

Asia WGS AF: 0.129 AC: 448 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.54
DANN	Benign	0.65
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1606116; hg19: chr2-160850515;