rs3087494

Variant names:

• chr4-109710465-A-G
• rs3087494
• NM_030821.5:c.*3912T>C

Your query was ambiguous. Multiple possible variants found:

• chr4-109710465-A-G
• chr4-109710465-A-T

Variant summary

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

The NM_030821.5(PLA2G12A):​c.*3912T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.489 in 152,084 control chromosomes in the GnomAD database, including 18,773 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 0.49 (18773 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: PLA2G12A NM_030821.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.976
• Publications: 11 publications found

Genes affected

PLA2G12A (HGNC:18554): (phospholipase A2 group XIIA) Secreted phospholipase A2 (sPLA2) enzymes liberate arachidonic acid from phospholipids for production of eicosanoids and exert a variety of physiologic and pathologic effects. Group XII sPLA2s, such as PLA2G12A, have relatively low specific activity and are structurally and functionally distinct from other sPLA2s (Gelb et al., 2000 [PubMed 11031251]).[supplied by OMIM, Mar 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLA2G12A	NM_030821.5	c.*3912T>C		3_prime_UTR_variant	Exon 4 of 4	ENST00000243501.10	NP_110448.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLA2G12A	ENST00000243501.10	c.*3912T>C		3_prime_UTR_variant	Exon 4 of 4	1	NM_030821.5	ENSP00000243501.5

Frequencies

GnomAD3 genomes AF: 0.489 AC: 74327 AN: 151966 Hom.: 18762 Cov.: 33

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.491

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.489 AC: 74370 AN: 152084 Hom.: 18773 Cov.: 33 AF XY: 0.491 AC XY: 36496 AN XY: 74354

African (AFR) AF: 0.353 AC: 14652 AN: 41490

American (AMR) AF: 0.486 AC: 7432 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.501 AC: 1741 AN: 3472

East Asian (EAS) AF: 0.481 AC: 2489 AN: 5178

South Asian (SAS) AF: 0.609 AC: 2939 AN: 4822

European-Finnish (FIN) AF: 0.569 AC: 6018 AN: 10574

Middle Eastern (MID) AF: 0.507 AC: 147 AN: 290

European-Non Finnish (NFE) AF: 0.549 AC: 37309 AN: 67946

Other (OTH) AF: 0.490 AC: 1037 AN: 2116

Alfa AF: 0.528 Hom.: 77790

Bravo AF: 0.474

Asia WGS AF: 0.548 AC: 1903 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.0
DANN	Benign	0.47
PhyloP100		0.98
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: rs3087494; hg19: chr4-110631621;