1-153347896-T-G
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_020393.4(PGLYRP4):c.37A>C(p.Ile13Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.84 in 1,611,302 control chromosomes in the GnomAD database, including 570,217 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 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_020393.4 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 |
---|---|---|---|---|---|---|---|
PGLYRP4 | NM_020393.4 | c.37A>C | p.Ile13Leu | missense_variant | 2/9 | ENST00000359650.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PGLYRP4 | ENST00000359650.10 | c.37A>C | p.Ile13Leu | missense_variant | 2/9 | 1 | NM_020393.4 | P4 | |
PGLYRP4 | ENST00000368739.3 | c.37A>C | p.Ile13Leu | missense_variant | 2/9 | 5 | A1 | ||
PGLYRP4 | ENST00000490266.1 | n.83A>C | non_coding_transcript_exon_variant | 1/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.810 AC: 123000AN: 151938Hom.: 50103 Cov.: 31
GnomAD3 exomes AF: 0.823 AC: 205999AN: 250354Hom.: 85097 AF XY: 0.827 AC XY: 111939AN XY: 135350
GnomAD4 exome AF: 0.843 AC: 1230842AN: 1459246Hom.: 520094 Cov.: 38 AF XY: 0.843 AC XY: 612398AN XY: 726050
GnomAD4 genome ? AF: 0.809 AC: 123065AN: 152056Hom.: 50123 Cov.: 31 AF XY: 0.811 AC XY: 60286AN XY: 74352
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at