chr6-46714342-A-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_005084.4(PLA2G7):​c.470+118T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 30)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

PLA2G7
NM_005084.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.368

Publications

17 publications found
Variant links:
Genes affected
PLA2G7 (HGNC:9040): (phospholipase A2 group VII) The protein encoded by this gene is a secreted enzyme that catalyzes the degradation of platelet-activating factor to biologically inactive products. Defects in this gene are a cause of platelet-activating factor acetylhydrolase deficiency. Two transcript variants encoding the same protein have been found for this gene.[provided by RefSeq, Dec 2009]

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PLA2G7NM_005084.4 linkc.470+118T>C intron_variant Intron 5 of 11 ENST00000274793.12 NP_005075.3 Q13093

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PLA2G7ENST00000274793.12 linkc.470+118T>C intron_variant Intron 5 of 11 1 NM_005084.4 ENSP00000274793.7 Q13093
PLA2G7ENST00000537365.1 linkc.470+118T>C intron_variant Intron 5 of 11 1 ENSP00000445666.1 Q13093

Frequencies

GnomAD3 genomes
Cov.:
30
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
0.00
AC:
0
AN:
625046
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
340238
African (AFR)
AF:
0.00
AC:
0
AN:
17648
American (AMR)
AF:
0.00
AC:
0
AN:
42378
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
20900
East Asian (EAS)
AF:
0.00
AC:
0
AN:
35678
South Asian (SAS)
AF:
0.00
AC:
0
AN:
68452
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
44174
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
4146
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
358588
Other (OTH)
AF:
0.00
AC:
0
AN:
33082
GnomAD4 genome
Cov.:
30
Alfa
AF:
0.00000238
Hom.:
138389

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.62
DANN
Benign
0.65
PhyloP100
-0.37

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

Publications

Other links and lift over

dbSNP: rs1362931; hg19: chr6-46682079; API