19-4013194-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_015897.4(PIAS4):c.299C>T(p.Pro100Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000242 in 1,613,402 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 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 -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PIAS4 | ENST00000262971.3 | c.299C>T | p.Pro100Leu | missense_variant | Exon 2 of 11 | 1 | NM_015897.4 | ENSP00000262971.1 | ||
PIAS4 | ENST00000593518.1 | n.302C>T | non_coding_transcript_exon_variant | Exon 2 of 3 | 4 | |||||
PIAS4 | ENST00000599999.5 | n.306C>T | non_coding_transcript_exon_variant | Exon 2 of 4 | 3 | |||||
PIAS4 | ENST00000600566.5 | n.304C>T | non_coding_transcript_exon_variant | Exon 2 of 4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152186Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251094Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135834
GnomAD4 exome AF: 0.0000233 AC: 34AN: 1461216Hom.: 0 Cov.: 32 AF XY: 0.0000275 AC XY: 20AN XY: 726932
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152186Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.299C>T (p.P100L) 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 299, causing the proline (P) at amino acid position 100 to be replaced by a leucine (L). 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