1-185301020-G-A
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Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_006469.5(IVNS1ABP):c.1072C>T(p.Arg358Ter) variant causes a stop gained change. The variant allele was found at a frequency of 0.000000684 in 1,461,268 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 6.8e-7 ( 0 hom. )
Consequence
IVNS1ABP
NM_006469.5 stop_gained
NM_006469.5 stop_gained
Scores
5
1
1
Clinical Significance
Conservation
PhyloP100: 5.34
Genes affected
IVNS1ABP (HGNC:16951): (influenza virus NS1A binding protein) Involved in RNA splicing; negative regulation of protein ubiquitination; and response to virus. Located in cytosol. Implicated in immunodeficiency 70. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 11 ACMG points.
PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 1-185301020-G-A is Pathogenic according to our data. Variant chr1-185301020-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 974683.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IVNS1ABP | NM_006469.5 | c.1072C>T | p.Arg358Ter | stop_gained | 10/15 | ENST00000367498.8 | |
IVNS1ABP | XM_047434070.1 | c.1072C>T | p.Arg358Ter | stop_gained | 10/15 | ||
IVNS1ABP | XM_047434096.1 | c.805C>T | p.Arg269Ter | stop_gained | 9/14 | ||
IVNS1ABP | XM_047434109.1 | c.418C>T | p.Arg140Ter | stop_gained | 4/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IVNS1ABP | ENST00000367498.8 | c.1072C>T | p.Arg358Ter | stop_gained | 10/15 | 1 | NM_006469.5 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
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32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250886Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135570
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GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461268Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 726934
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GnomAD4 genome Cov.: 32
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Immunodeficiency 70 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jul 31, 2020 | - - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
MutationTaster
Benign
A;A
Vest4
GERP RS
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at