chr19-48062024-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_003706.3(PLA2G4C):c.1231G>A(p.Asp411Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000813 in 1,613,742 control chromosomes in the GnomAD database, including 13 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_003706.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLA2G4C | NM_003706.3 | c.1231G>A | p.Asp411Asn | missense_variant | 14/17 | ENST00000599921.6 | |
PLA2G4C-AS1 | NR_132363.1 | n.320C>T | non_coding_transcript_exon_variant | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLA2G4C | ENST00000599921.6 | c.1231G>A | p.Asp411Asn | missense_variant | 14/17 | 1 | NM_003706.3 | A2 | |
PLA2G4C-AS1 | ENST00000596552.1 | n.263C>T | non_coding_transcript_exon_variant | 3/5 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00412 AC: 627AN: 152024Hom.: 5 Cov.: 32
GnomAD3 exomes AF: 0.00106 AC: 266AN: 251172Hom.: 2 AF XY: 0.000751 AC XY: 102AN XY: 135754
GnomAD4 exome AF: 0.000468 AC: 684AN: 1461600Hom.: 8 Cov.: 31 AF XY: 0.000396 AC XY: 288AN XY: 727098
GnomAD4 genome ? AF: 0.00413 AC: 628AN: 152142Hom.: 5 Cov.: 32 AF XY: 0.00378 AC XY: 281AN XY: 74360
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Apr 04, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at