chr1-20068908-C-G

Position:

• chr1-20068908-C-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The XM_005245891.6(PLA2G5):​c.-42C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000144 in 1,286,040 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.00067 (0 hom., cov: 31)
  • Exomes 𝑓: 0.000073 (0 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

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLA2G5	XM_005245891.6	c.-42C>G		5_prime_UTR_variant	4/8		XP_005245948.1
PLA2G5	XM_005245892.6	c.-42C>G		5_prime_UTR_variant	3/7		XP_005245949.1
PLA2G5	XM_005245893.6	c.-307C>G		5_prime_UTR_variant	3/8		XP_005245950.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLA2G5	ENST00000460175.5	n.373C>G		non_coding_transcript_exon_variant	3/7	3
PLA2G5	ENST00000465698.5	n.377C>G		non_coding_transcript_exon_variant	3/8	3
PLA2G5	ENST00000469069.5	n.400C>G		non_coding_transcript_exon_variant	4/7	3

Frequencies

GnomAD3 genomes AF: 0.000671 AC: 102 AN: 151940 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.00235

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000131

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.000478

GnomAD3 exomes AF: 0.000180 AC: 24 AN: 133684 Hom.: 0 AF XY: 0.000137 AC XY: 10 AN XY: 72780

Gnomad AFR exome AF: 0.00202

Gnomad AMR exome AF: 0.000205

Gnomad ASJ exome AF: 0.000121

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0000892

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000382

Gnomad OTH exome AF: 0.000243

GnomAD4 exome AF: 0.0000732 AC: 83 AN: 1133982 Hom.: 0 Cov.: 27 AF XY: 0.0000647 AC XY: 36 AN XY: 556532

Gnomad4 AFR exome AF: 0.00209

Gnomad4 AMR exome AF: 0.000284

Gnomad4 ASJ exome AF: 0.0000629

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000658

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000174

Gnomad4 OTH exome AF: 0.0000483

GnomAD4 genome AF: 0.000671 AC: 102 AN: 152058 Hom.: 0 Cov.: 31 AF XY: 0.000700 AC XY: 52 AN XY: 74310

Gnomad4 AFR AF: 0.00234

Gnomad4 AMR AF: 0.000131

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.000208

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.000473

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.66
DANN	Benign	0.56

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;