chr15-68086683-G-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_016166.3(PIAS1):c.402G>A(p.Pro134=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,613,224 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
Genomes: 𝑓 0.000039 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000012 ( 0 hom. )
Consequence
PIAS1
NM_016166.3 synonymous
NM_016166.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.49
Genes affected
PIAS1 (HGNC:2752): (protein inhibitor of activated STAT 1) This gene encodes a member of the protein inhibitor of activated STAT (PIAS) family. PIAS proteins function as SUMO E3 ligases and play important roles in many cellular processes by mediating the sumoylation of target proteins. This protein plays a central role as a transcriptional coregulator of numerous cellular pathways includign the STAT1 and nuclear factor kappaB pathways. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.45).
BP6
?
Variant 15-68086683-G-A is Benign according to our data. Variant chr15-68086683-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1597974.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=1.49 with no splicing effect.
BS2
?
High AC in GnomAd at 6 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIAS1 | NM_016166.3 | c.402G>A | p.Pro134= | synonymous_variant | 2/14 | ENST00000249636.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIAS1 | ENST00000249636.11 | c.402G>A | p.Pro134= | synonymous_variant | 2/14 | 1 | NM_016166.3 | P1 | |
PIAS1 | ENST00000545237.1 | c.408G>A | p.Pro136= | synonymous_variant | 3/15 | 2 | |||
PIAS1 | ENST00000564915.5 | c.402G>A | p.Pro134= | synonymous_variant, NMD_transcript_variant | 2/5 | 5 | |||
PIAS1 | ENST00000562190.1 | c.*492G>A | 3_prime_UTR_variant, NMD_transcript_variant | 4/6 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000395 AC: 6AN: 152014Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000241 AC: 6AN: 248856Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 134996
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GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461210Hom.: 0 Cov.: 30 AF XY: 0.00000550 AC XY: 4AN XY: 726934
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GnomAD4 genome ? AF: 0.0000395 AC: 6AN: 152014Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74234
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 29, 2021 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at