2-232524355-G-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_001195129.2(PRSS56):c.1400G>T(p.Arg467Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000296 in 1,535,512 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 9/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001195129.2 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PRSS56 | NM_001195129.2 | c.1400G>T | p.Arg467Leu | missense_variant | Exon 11 of 13 | ENST00000617714.2 | NP_001182058.1 | |
PRSS56 | NM_001369848.1 | c.1403G>T | p.Arg468Leu | missense_variant | Exon 11 of 13 | NP_001356777.1 | ||
PRSS56 | XM_047445431.1 | c.1496G>T | p.Arg499Leu | missense_variant | Exon 10 of 12 | XP_047301387.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00122 AC: 185AN: 152244Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000378 AC: 50AN: 132316Hom.: 2 AF XY: 0.000319 AC XY: 23AN XY: 72106
GnomAD4 exome AF: 0.000194 AC: 269AN: 1383150Hom.: 4 Cov.: 36 AF XY: 0.000179 AC XY: 122AN XY: 682460
GnomAD4 genome AF: 0.00122 AC: 186AN: 152362Hom.: 0 Cov.: 34 AF XY: 0.00125 AC XY: 93AN XY: 74508
ClinVar
Submissions by phenotype
Isolated microphthalmia 6 Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre | Mar 25, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 29, 2025 | - - |
not provided Pathogenic:1
Likely pathogenic, flagged submission | research | Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at