chr1-43958811-A-G
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_014652.4(IPO13):c.1950A>G(p.Thr650=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00265 in 1,613,938 control chromosomes in the GnomAD database, including 101 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.014 ( 61 hom., cov: 32)
Exomes 𝑓: 0.0014 ( 40 hom. )
Consequence
IPO13
NM_014652.4 synonymous
NM_014652.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.30
Genes affected
IPO13 (HGNC:16853): (importin 13) This gene encodes a member of the importin-beta family of nuclear transport proteins. The encoded protein mediates the import of specific cargo proteins from the cytoplasm to the nucleus and is dependent on the Ras-related nuclear protein-GTPase system. The encoded protein is also involved in nuclear export of the eukaryotic translation initiation factor 1A.[provided by RefSeq, Mar 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
?
Variant 1-43958811-A-G is Benign according to our data. Variant chr1-43958811-A-G is described in ClinVar as [Benign]. Clinvar id is 775544.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-2.3 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0144 (2192/152090) while in subpopulation AFR AF= 0.0503 (2086/41450). AF 95% confidence interval is 0.0485. There are 61 homozygotes in gnomad4. There are 1019 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 2190 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IPO13 | NM_014652.4 | c.1950A>G | p.Thr650= | synonymous_variant | 11/20 | ENST00000372343.8 | |
IPO13 | XM_024451069.2 | c.1047A>G | p.Thr349= | synonymous_variant | 10/19 | ||
IPO13 | XM_024451070.2 | c.1047A>G | p.Thr349= | synonymous_variant | 10/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IPO13 | ENST00000372343.8 | c.1950A>G | p.Thr650= | synonymous_variant | 11/20 | 1 | NM_014652.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0144 AC: 2190AN: 151972Hom.: 61 Cov.: 32
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GnomAD3 exomes AF: 0.00372 AC: 934AN: 251090Hom.: 31 AF XY: 0.00284 AC XY: 386AN XY: 135710
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GnomAD4 exome AF: 0.00143 AC: 2092AN: 1461848Hom.: 40 Cov.: 33 AF XY: 0.00121 AC XY: 879AN XY: 727224
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GnomAD4 genome ? AF: 0.0144 AC: 2192AN: 152090Hom.: 61 Cov.: 32 AF XY: 0.0137 AC XY: 1019AN XY: 74362
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
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
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at