rs2148911

Variant names:

• chr1-20069094-G-A
• rs2148911
• ENST00000962171.1:c.-235G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-20069094-G-A
• chr1-20069094-G-C
• chr1-20069094-G-T

Variant summary

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

The ENST00000962171.1(PLA2G5):​c.-235G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0777 in 467,400 control chromosomes in the GnomAD database, including 2,092 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 0.062 (488 hom., cov: 32)
  • Exomes 𝑓: 0.085 (1604 hom.)
• Consequence: PLA2G5 ENST00000962171.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.931
• Publications: 7 publications found

Genes affected

PLA2G5 (HGNC:9038): (phospholipase A2 group V) This gene is a member of the secretory phospholipase A2 family. It is located in a tightly-linked cluster of secretory phospholipase A2 genes on chromosome 1. The encoded enzyme catalyzes the hydrolysis of membrane phospholipids to generate lysophospholipids and free fatty acids including arachidonic acid. It preferentially hydrolyzes linoleoyl-containing phosphatidylcholine substrates. Secretion of this enzyme is thought to induce inflammatory responses in neighboring cells. Alternatively spliced transcript variants have been found, but their full-length nature has not been determined. [provided by RefSeq, Jul 2008]

PLA2G5 Gene-Disease associations (from GenCC):

• familial benign flecked retina

  Inheritance: AR Classification: DEFINITIVE, SUPPORTIVE, LIMITED Submitted by: G2P, Ambry Genetics, Orphanet
• late-adult onset retinitis pigmentosa

  Inheritance: AR Classification: LIMITED Submitted by: Franklin by Genoox

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000962171.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLA2G5	ENST00000962171.1		c.-235G>A		5_prime_UTR	Exon 3 of 7	ENSP00000632230.1
	PLA2G5	ENST00000894073.1		c.-11+62G>A		intron	N/A	ENSP00000564132.1
	PLA2G5	ENST00000894074.1		c.-183+62G>A		intron	N/A	ENSP00000564133.1

Frequencies

GnomAD3 genomes AF: 0.0625 AC: 9512 AN: 152084 Hom.: 491 Cov.: 32

Gnomad AFR AF: 0.0216

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.0659

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0539

Gnomad OTH AF: 0.0578

GnomAD4 exome AF: 0.0850 AC: 26799 AN: 315198 Hom.: 1604 AF XY: 0.0889 AC XY: 15870 AN XY: 178462

African (AFR) AF: 0.0181 AC: 160 AN: 8838

American (AMR) AF: 0.135 AC: 3649 AN: 27008

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 1229 AN: 10746

East Asian (EAS) AF: 0.261 AC: 2395 AN: 9180

South Asian (SAS) AF: 0.127 AC: 7543 AN: 59420

European-Finnish (FIN) AF: 0.0594 AC: 758 AN: 12760

Middle Eastern (MID) AF: 0.164 AC: 461 AN: 2804

European-Non Finnish (NFE) AF: 0.0556 AC: 9437 AN: 169850

Other (OTH) AF: 0.0800 AC: 1167 AN: 14592

GnomAD4 genome AF: 0.0624 AC: 9500 AN: 152202 Hom.: 488 Cov.: 32 AF XY: 0.0673 AC XY: 5007 AN XY: 74402

African (AFR) AF: 0.0216 AC: 896 AN: 41550

American (AMR) AF: 0.110 AC: 1683 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 429 AN: 3468

East Asian (EAS) AF: 0.254 AC: 1311 AN: 5160

South Asian (SAS) AF: 0.132 AC: 638 AN: 4824

European-Finnish (FIN) AF: 0.0659 AC: 698 AN: 10594

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0539 AC: 3665 AN: 68018

Other (OTH) AF: 0.0568 AC: 120 AN: 2114

Alfa AF: 0.0519 Hom.: 139

Bravo AF: 0.0632

Asia WGS AF: 0.167 AC: 581 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.80
DANN	Benign	0.42
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs2148911; hg19: chr1-20395587; COSMIC: COSV64282876;