19-4013289-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_015897.4(PIAS4):c.394C>T(p.Arg132Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000186 in 1,613,216 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015897.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PIAS4 | ENST00000262971.3 | c.394C>T | p.Arg132Cys | missense_variant | Exon 2 of 11 | 1 | NM_015897.4 | ENSP00000262971.1 | ||
PIAS4 | ENST00000593518.1 | n.397C>T | non_coding_transcript_exon_variant | Exon 2 of 3 | 4 | |||||
PIAS4 | ENST00000599999.5 | n.401C>T | non_coding_transcript_exon_variant | Exon 2 of 4 | 3 | |||||
PIAS4 | ENST00000600566.5 | n.399C>T | non_coding_transcript_exon_variant | Exon 2 of 4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152152Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000280 AC: 7AN: 250308Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135650
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1460946Hom.: 0 Cov.: 32 AF XY: 0.0000138 AC XY: 10AN XY: 726792
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152270Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74460
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.394C>T (p.R132C) alteration is located in exon 2 (coding exon 2) of the PIAS4 gene. This alteration results from a C to T substitution at nucleotide position 394, causing the arginine (R) at amino acid position 132 to be replaced by a cysteine (C). 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