rs11573185

Variant names:

• chr1-20068908-C-A
• rs11573185
• XM_005245891.6:c.-42C>A

Your query was ambiguous. Multiple possible variants found:

• chr1-20068908-C-A
• chr1-20068908-C-G
• chr1-20068908-C-T

Variant summary

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

The XM_005245891.6(PLA2G5):​c.-42C>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 0.523 in 1,281,692 control chromosomes in the GnomAD database, including 179,473 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 0.46 (17261 hom., cov: 31)
  • Exomes 𝑓: 0.53 (162212 hom.)
• Consequence: PLA2G5 XM_005245891.6 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.229

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.547 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLA2G5	XM_005245891.6	c.-42C>A		5_prime_UTR_variant	Exon 4 of 8		XP_005245948.1
PLA2G5	XM_005245892.6	c.-42C>A		5_prime_UTR_variant	Exon 3 of 7		XP_005245949.1
PLA2G5	XM_011541586.4	c.-42C>A		5_prime_UTR_variant	Exon 2 of 6		XP_011539888.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLA2G5	ENST00000460175.5	n.373C>A		non_coding_transcript_exon_variant	Exon 3 of 7	3
PLA2G5	ENST00000465698.5	n.377C>A		non_coding_transcript_exon_variant	Exon 3 of 8	3
PLA2G5	ENST00000469069.5	n.400C>A		non_coding_transcript_exon_variant	Exon 4 of 7	3

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69409 AN: 151870 Hom.: 17232 Cov.: 31

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.483

GnomAD2 exomes AF: 0.517 AC: 69057 AN: 133684 AF XY: 0.518

Gnomad AFR exome AF: 0.234

Gnomad AMR exome AF: 0.591

Gnomad ASJ exome AF: 0.487

Gnomad EAS exome AF: 0.371

Gnomad FIN exome AF: 0.553

Gnomad NFE exome AF: 0.548

Gnomad OTH exome AF: 0.536

GnomAD4 exome AF: 0.532 AC: 600447 AN: 1129704 Hom.: 162212 Cov.: 27 AF XY: 0.532 AC XY: 294959 AN XY: 554636

Gnomad4 AFR exome AF: 0.228 AC: 5536 AN: 24308

Gnomad4 AMR exome AF: 0.592 AC: 16688 AN: 28194

Gnomad4 ASJ exome AF: 0.492 AC: 7805 AN: 15874

Gnomad4 EAS exome AF: 0.372 AC: 4768 AN: 12808

Gnomad4 SAS exome AF: 0.505 AC: 38389 AN: 75946

Gnomad4 FIN exome AF: 0.550 AC: 7190 AN: 13062

Gnomad4 NFE exome AF: 0.543 AC: 496512 AN: 913810

Gnomad4 Remaining exome AF: 0.512 AC: 21154 AN: 41316

GnomAD4 genome AF: 0.457 AC: 69490 AN: 151988 Hom.: 17261 Cov.: 31 AF XY: 0.457 AC XY: 33940 AN XY: 74272

Gnomad4 AFR AF: 0.246 AC: 0.245948 AN: 0.245948

Gnomad4 AMR AF: 0.557 AC: 0.55712 AN: 0.55712

Gnomad4 ASJ AF: 0.484 AC: 0.484438 AN: 0.484438

Gnomad4 EAS AF: 0.388 AC: 0.387984 AN: 0.387984

Gnomad4 SAS AF: 0.481 AC: 0.481312 AN: 0.481312

Gnomad4 FIN AF: 0.533 AC: 0.533441 AN: 0.533441

Gnomad4 NFE AF: 0.550 AC: 0.549768 AN: 0.549768

Gnomad4 OTH AF: 0.488 AC: 0.487689 AN: 0.487689

Alfa AF: 0.516 Hom.: 37477

Bravo AF: 0.451

Asia WGS AF: 0.447 AC: 1555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.0
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11573185; hg19: chr1-20395401; COSMIC: COSV64283089;