chr1-153330814-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020393.4(PGLYRP4):c.1075C>A(p.Gln359Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000018 in 1,613,896 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 (★).
Frequency
Consequence
NM_020393.4 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 | UniProt |
---|---|---|---|---|---|---|---|
PGLYRP4 | NM_020393.4 | c.1075C>A | p.Gln359Lys | missense_variant | 9/9 | ENST00000359650.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PGLYRP4 | ENST00000359650.10 | c.1075C>A | p.Gln359Lys | missense_variant | 9/9 | 1 | NM_020393.4 | P4 | |
PGLYRP4 | ENST00000368739.3 | c.1063C>A | p.Gln355Lys | missense_variant | 9/9 | 5 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152096Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251330Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135830
GnomAD4 exome AF: 0.0000185 AC: 27AN: 1461800Hom.: 0 Cov.: 31 AF XY: 0.0000261 AC XY: 19AN XY: 727210
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152096Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74292
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 05, 2022 | The c.1075C>A (p.Q359K) alteration is located in exon 9 (coding exon 8) of the PGLYRP4 gene. This alteration results from a C to A substitution at nucleotide position 1075, causing the glutamine (Q) at amino acid position 359 to be replaced by a lysine (K). 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