1-185307118-T-G
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 1P and 5B. PP2BP4BS2
The NM_006469.5(IVNS1ABP):āc.553A>Cā(p.Asn185His) variant causes a missense change. The variant allele was found at a frequency of 0.00000806 in 1,613,360 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 (ā ).
Frequency
Genomes: š 0.000020 ( 0 hom., cov: 32)
Exomes š: 0.0000068 ( 0 hom. )
Consequence
IVNS1ABP
NM_006469.5 missense
NM_006469.5 missense
Scores
1
5
13
Clinical Significance
Conservation
PhyloP100: 6.08
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 Likely_benign. Variant got -4 ACMG points.
PP2
Missense variant where missense usually causes diseases, IVNS1ABP
BP4
Computational evidence support a benign effect (MetaRNN=0.36117762).
BS2
High AC in GnomAdExome4 at 10 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IVNS1ABP | NM_006469.5 | c.553A>C | p.Asn185His | missense_variant | 7/15 | ENST00000367498.8 | |
IVNS1ABP | XM_047434070.1 | c.553A>C | p.Asn185His | missense_variant | 7/15 | ||
IVNS1ABP | XM_047434096.1 | c.286A>C | p.Asn96His | missense_variant | 6/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IVNS1ABP | ENST00000367498.8 | c.553A>C | p.Asn185His | missense_variant | 7/15 | 1 | NM_006469.5 | P1 | |
IVNS1ABP | ENST00000422754.1 | c.196A>C | p.Asn66His | missense_variant | 2/2 | 2 | |||
IVNS1ABP | ENST00000459929.5 | n.1120A>C | non_coding_transcript_exon_variant | 7/16 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152186Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00000797 AC: 2AN: 251066Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135676
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GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461174Hom.: 0 Cov.: 31 AF XY: 0.00000963 AC XY: 7AN XY: 726878
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GnomAD4 genome AF: 0.0000197 AC: 3AN: 152186Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74344
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 12, 2023 | The c.553A>C (p.N185H) alteration is located in exon 7 (coding exon 5) of the IVNS1ABP gene. This alteration results from a A to C substitution at nucleotide position 553, causing the asparagine (N) at amino acid position 185 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;.
Eigen
Uncertain
Eigen_PC
Benign
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;.
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N
REVEL
Uncertain
Sift
Benign
T;D
Sift4G
Benign
T;D
Polyphen
D;.
Vest4
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
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