rs1511217

Variant names:

• chr2-159958582-T-C
• rs1511217
• NM_007366.5:c.2905-1955A>G

Variant summary

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

The NM_007366.5(PLA2R1):​c.2905-1955A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 152,000 control chromosomes in the GnomAD database, including 2,858 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 0.18 (2858 hom., cov: 32)
• Consequence: PLA2R1 NM_007366.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.333
• Publications: 3 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.405 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.2905-1955A>G		intron	N/A	NP_031392.3
	PLA2R1	NM_001195641.2		c.2905-1955A>G		intron	N/A	NP_001182570.1	B7ZML4
	PLA2R1	NM_001007267.3		c.2905-1955A>G		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.2905-1955A>G		intron	N/A	ENSP00000283243.7	Q13018-1
	PLA2R1	ENST00000392771.1	TSL:1	c.2905-1955A>G		intron	N/A	ENSP00000376524.1	Q13018-2
	PLA2R1	ENST00000890090.1		c.2905-1955A>G		intron	N/A	ENSP00000560149.1

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27791 AN: 151880 Hom.: 2863 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.183 AC: 27794 AN: 152000 Hom.: 2858 Cov.: 32 AF XY: 0.188 AC XY: 13990 AN XY: 74320

African (AFR) AF: 0.104 AC: 4324 AN: 41458

American (AMR) AF: 0.175 AC: 2667 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 927 AN: 3464

East Asian (EAS) AF: 0.181 AC: 935 AN: 5162

South Asian (SAS) AF: 0.420 AC: 2022 AN: 4810

European-Finnish (FIN) AF: 0.201 AC: 2122 AN: 10564

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.208 AC: 14115 AN: 67970

Other (OTH) AF: 0.198 AC: 419 AN: 2114

Alfa AF: 0.206 Hom.: 5749

Bravo AF: 0.172

Asia WGS AF: 0.277 AC: 962 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.0
DANN	Benign	0.73
PhyloP100		-0.33
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: rs1511217; hg19: chr2-160815093;