rs11677

Variant names:

• chr1-19975471-G-A
• rs11677
• NM_001395463.1:c.*230C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-19975471-G-A
• chr1-19975471-G-C

Variant summary

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

The NM_001395463.1(PLA2G2A):​c.*230C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 585,588 control chromosomes in the GnomAD database, including 4,993 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 0.099 (1010 hom., cov: 32)
  • Exomes 𝑓: 0.13 (3983 hom.)
• Consequence: PLA2G2A NM_001395463.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.390
• Publications: 22 publications found

Genes affected

PLA2G2A (HGNC:9031): (phospholipase A2 group IIA) The protein encoded by this gene is a member of the phospholipase A2 family (PLA2). PLA2s constitute a diverse family of enzymes with respect to sequence, function, localization, and divalent cation requirements. This gene product belongs to group II, which contains secreted form of PLA2, an extracellular enzyme that has a low molecular mass and requires calcium ions for catalysis. It catalyzes the hydrolysis of the sn-2 fatty acid acyl ester bond of phosphoglycerides, releasing free fatty acids and lysophospholipids, and thought to participate in the regulation of the phospholipid metabolism in biomembranes. Several alternatively spliced transcript variants with different 5' UTRs have been found for this gene.[provided by RefSeq, Sep 2009]

PLA2G2A Gene-Disease associations (from GenCC):

• colorectal cancer

  Inheritance: AD Classification: LIMITED, NO_KNOWN Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLA2G2A	NM_001395463.1	c.*230C>T		3_prime_UTR_variant	Exon 5 of 5	ENST00000482011.3	NP_001382392.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLA2G2A	ENST00000482011.3	c.*230C>T		3_prime_UTR_variant	Exon 5 of 5	1	NM_001395463.1	ENSP00000504762.1

Frequencies

GnomAD3 genomes AF: 0.0992 AC: 15084 AN: 152102 Hom.: 1011 Cov.: 32

Gnomad AFR AF: 0.0235

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.0940

GnomAD4 exome AF: 0.128 AC: 55515 AN: 433368 Hom.: 3983 Cov.: 0 AF XY: 0.131 AC XY: 30075 AN XY: 229438

African (AFR) AF: 0.0230 AC: 278 AN: 12096

American (AMR) AF: 0.195 AC: 3594 AN: 18388

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 1578 AN: 13196

East Asian (EAS) AF: 0.187 AC: 5533 AN: 29566

South Asian (SAS) AF: 0.178 AC: 8118 AN: 45728

European-Finnish (FIN) AF: 0.106 AC: 3046 AN: 28854

Middle Eastern (MID) AF: 0.160 AC: 300 AN: 1870

European-Non Finnish (NFE) AF: 0.116 AC: 30088 AN: 258664

Other (OTH) AF: 0.119 AC: 2980 AN: 25006

GnomAD4 genome AF: 0.0990 AC: 15074 AN: 152220 Hom.: 1010 Cov.: 32 AF XY: 0.104 AC XY: 7726 AN XY: 74410

African (AFR) AF: 0.0235 AC: 975 AN: 41532

American (AMR) AF: 0.164 AC: 2502 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 423 AN: 3472

East Asian (EAS) AF: 0.174 AC: 900 AN: 5186

South Asian (SAS) AF: 0.182 AC: 875 AN: 4820

European-Finnish (FIN) AF: 0.125 AC: 1322 AN: 10584

Middle Eastern (MID) AF: 0.154 AC: 45 AN: 292

European-Non Finnish (NFE) AF: 0.114 AC: 7762 AN: 68016

Other (OTH) AF: 0.0930 AC: 196 AN: 2108

Alfa AF: 0.112 Hom.: 3566

Bravo AF: 0.0996

Asia WGS AF: 0.160 AC: 556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.6
DANN	Benign	0.53
PhyloP100		0.39
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: rs11677; hg19: chr1-20301964;