rs892145
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_052890.4(PGLYRP2):c.809T>A(p.Met270Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 1,613,702 control chromosomes in the GnomAD database, including 112,897 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_052890.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PGLYRP2 | NM_052890.4 | c.809T>A | p.Met270Lys | missense_variant | 2/5 | ENST00000340880.5 | |
PGLYRP2 | NM_001363546.1 | c.809T>A | p.Met270Lys | missense_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PGLYRP2 | ENST00000340880.5 | c.809T>A | p.Met270Lys | missense_variant | 2/5 | 1 | NM_052890.4 | P2 | |
PGLYRP2 | ENST00000292609.8 | c.809T>A | p.Met270Lys | missense_variant | 2/4 | 1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.378 AC: 57332AN: 151804Hom.: 10947 Cov.: 31
GnomAD3 exomes AF: 0.358 AC: 89600AN: 250436Hom.: 16258 AF XY: 0.356 AC XY: 48207AN XY: 135552
GnomAD4 exome AF: 0.372 AC: 543487AN: 1461780Hom.: 101948 Cov.: 67 AF XY: 0.370 AC XY: 269263AN XY: 727190
GnomAD4 genome ? AF: 0.378 AC: 57378AN: 151922Hom.: 10949 Cov.: 31 AF XY: 0.381 AC XY: 28276AN XY: 74228
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at