2-159956524-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_007366.5(PLA2R1):c.3008G>A(p.Ser1003Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000305 in 1,606,980 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_007366.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLA2R1 | NM_007366.5 | c.3008G>A | p.Ser1003Asn | missense_variant | 21/30 | ENST00000283243.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLA2R1 | ENST00000283243.13 | c.3008G>A | p.Ser1003Asn | missense_variant | 21/30 | 1 | NM_007366.5 | P1 | |
PLA2R1 | ENST00000392771.1 | c.3008G>A | p.Ser1003Asn | missense_variant | 21/27 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000184 AC: 28AN: 152210Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251276Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135800
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1454652Hom.: 0 Cov.: 28 AF XY: 0.00000828 AC XY: 6AN XY: 724232
GnomAD4 genome ? AF: 0.000184 AC: 28AN: 152328Hom.: 0 Cov.: 32 AF XY: 0.000201 AC XY: 15AN XY: 74484
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 20, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at