19-4028743-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_015897.4(PIAS4):c.696C>T(p.Pro232Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000502 in 1,612,410 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 Likely benign (★).
Frequency
Consequence
NM_015897.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PIAS4 | NM_015897.4 | c.696C>T | p.Pro232Pro | synonymous_variant | Exon 6 of 11 | ENST00000262971.3 | NP_056981.2 | |
PIAS4 | XM_011528060.3 | c.753C>T | p.Pro251Pro | synonymous_variant | Exon 6 of 11 | XP_011526362.1 | ||
PIAS4 | XM_017026868.2 | c.123C>T | p.Pro41Pro | synonymous_variant | Exon 3 of 8 | XP_016882357.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PIAS4 | ENST00000262971.3 | c.696C>T | p.Pro232Pro | synonymous_variant | Exon 6 of 11 | 1 | NM_015897.4 | ENSP00000262971.1 | ||
PIAS4 | ENST00000596144.1 | n.544C>T | non_coding_transcript_exon_variant | Exon 5 of 5 | 3 | |||||
PIAS4 | ENST00000601439.1 | n.164C>T | non_coding_transcript_exon_variant | Exon 2 of 2 | 3 | |||||
PIAS4 | ENST00000599999.5 | n.*156C>T | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152100Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000844 AC: 21AN: 248818Hom.: 0 AF XY: 0.000126 AC XY: 17AN XY: 134856
GnomAD4 exome AF: 0.0000500 AC: 73AN: 1460310Hom.: 0 Cov.: 35 AF XY: 0.0000619 AC XY: 45AN XY: 726398
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152100Hom.: 0 Cov.: 30 AF XY: 0.0000538 AC XY: 4AN XY: 74292
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at