chr19-48074825-A-G
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_003706.3(PLA2G4C):c.948T>C(p.Asn316=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00253 in 1,612,898 control chromosomes in the GnomAD database, including 95 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.013 ( 54 hom., cov: 31)
Exomes 𝑓: 0.0014 ( 41 hom. )
Consequence
PLA2G4C
NM_003706.3 synonymous
NM_003706.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.34
Genes affected
PLA2G4C (HGNC:9037): (phospholipase A2 group IVC) This gene encodes a protein which is a member of the phospholipase A2 enzyme family which hydrolyzes glycerophospholipids to produce free fatty acids and lysophospholipids, both of which serve as precursors in the production of signaling molecules. The encoded protein has been shown to be a calcium-independent and membrane bound enzyme. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2009]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BP6
?
Variant 19-48074825-A-G is Benign according to our data. Variant chr19-48074825-A-G is described in ClinVar as [Benign]. Clinvar id is 788028.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-1.34 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0134 (2040/152120) while in subpopulation AFR AF= 0.0466 (1931/41478). AF 95% confidence interval is 0.0448. There are 54 homozygotes in gnomad4. There are 985 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 53 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLA2G4C | NM_003706.3 | c.948T>C | p.Asn316= | synonymous_variant | 12/17 | ENST00000599921.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLA2G4C | ENST00000599921.6 | c.948T>C | p.Asn316= | synonymous_variant | 12/17 | 1 | NM_003706.3 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0134 AC: 2031AN: 152002Hom.: 53 Cov.: 31
GnomAD3 genomes
?
AF:
AC:
2031
AN:
152002
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.00384 AC: 961AN: 250102Hom.: 19 AF XY: 0.00297 AC XY: 401AN XY: 135170
GnomAD3 exomes
AF:
AC:
961
AN:
250102
Hom.:
AF XY:
AC XY:
401
AN XY:
135170
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00140 AC: 2048AN: 1460778Hom.: 41 Cov.: 30 AF XY: 0.00123 AC XY: 892AN XY: 726678
GnomAD4 exome
AF:
AC:
2048
AN:
1460778
Hom.:
Cov.:
30
AF XY:
AC XY:
892
AN XY:
726678
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.0134 AC: 2040AN: 152120Hom.: 54 Cov.: 31 AF XY: 0.0132 AC XY: 985AN XY: 74352
GnomAD4 genome
?
AF:
AC:
2040
AN:
152120
Hom.:
Cov.:
31
AF XY:
AC XY:
985
AN XY:
74352
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at