chr2-159949706-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_007366.5(PLA2R1):c.3611C>T(p.Ser1204Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,613,602 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S1204C) has been classified as Uncertain significance.
Frequency
Consequence
NM_007366.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLA2R1 | NM_007366.5 | c.3611C>T | p.Ser1204Phe | missense_variant | 25/30 | ENST00000283243.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLA2R1 | ENST00000283243.13 | c.3611C>T | p.Ser1204Phe | missense_variant | 25/30 | 1 | NM_007366.5 | P1 | |
PLA2R1 | ENST00000392771.1 | c.3611C>T | p.Ser1204Phe | missense_variant | 25/27 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152202Hom.: 0 Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461400Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 727032
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152202Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 12, 2022 | The c.3611C>T (p.S1204F) alteration is located in exon 25 (coding exon 25) of the PLA2R1 gene. This alteration results from a C to T substitution at nucleotide position 3611, causing the serine (S) at amino acid position 1204 to be replaced by a phenylalanine (F). 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