2-159945014-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000283243.13(PLA2R1):āc.4036A>Gā(p.Thr1346Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000304 in 1,613,624 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
ENST00000283243.13 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PLA2R1 | NM_007366.5 | c.4036A>G | p.Thr1346Ala | missense_variant | 28/30 | ENST00000283243.13 | NP_031392.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLA2R1 | ENST00000283243.13 | c.4036A>G | p.Thr1346Ala | missense_variant | 28/30 | 1 | NM_007366.5 | ENSP00000283243 | P1 | |
PLA2R1 | ENST00000460710.2 | upstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152130Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 251298Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135818
GnomAD4 exome AF: 0.0000308 AC: 45AN: 1461494Hom.: 0 Cov.: 30 AF XY: 0.0000289 AC XY: 21AN XY: 727056
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152130Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74318
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 03, 2022 | The c.4036A>G (p.T1346A) alteration is located in exon 28 (coding exon 28) of the PLA2R1 gene. This alteration results from a A to G substitution at nucleotide position 4036, causing the threonine (T) at amino acid position 1346 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at