19-46019609-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_005091.3(PGLYRP1):c.326G>A(p.Arg109His) variant causes a missense change. The variant allele was found at a frequency of 0.0000514 in 1,613,820 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 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. R109C) has been classified as Uncertain significance.
Frequency
Consequence
NM_005091.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152122Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251114Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135732
GnomAD4 exome AF: 0.0000520 AC: 76AN: 1461698Hom.: 0 Cov.: 33 AF XY: 0.0000481 AC XY: 35AN XY: 727168
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152122Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74286
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.326G>A (p.R109H) alteration is located in exon 2 (coding exon 2) of the PGLYRP1 gene. This alteration results from a G to A substitution at nucleotide position 326, causing the arginine (R) at amino acid position 109 to be replaced by a histidine (H). 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