2-61496870-T-C
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_003400.4(XPO1):c.888+9A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0014 in 1,577,470 control chromosomes in the GnomAD database, including 35 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0077 ( 20 hom., cov: 32)
Exomes 𝑓: 0.00074 ( 15 hom. )
Consequence
XPO1
NM_003400.4 intron
NM_003400.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.313
Genes affected
XPO1 (HGNC:12825): (exportin 1) This cell-cycle-regulated gene encodes a protein that mediates leucine-rich nuclear export signal (NES)-dependent protein transport. The protein specifically inhibits the nuclear export of Rev and U snRNAs. It is involved in the control of several cellular processes by controlling the localization of cyclin B, MPAK, and MAPKAP kinase 2. This protein also regulates NFAT and AP-1. [provided by RefSeq, Jan 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
Variant 2-61496870-T-C is Benign according to our data. Variant chr2-61496870-T-C is described in ClinVar as [Benign]. Clinvar id is 775721.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00767 (1168/152366) while in subpopulation AFR AF= 0.0269 (1118/41586). AF 95% confidence interval is 0.0256. There are 20 homozygotes in gnomad4. There are 553 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 1168 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
XPO1 | NM_003400.4 | c.888+9A>G | intron_variant | ENST00000401558.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
XPO1 | ENST00000401558.7 | c.888+9A>G | intron_variant | 1 | NM_003400.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00767 AC: 1168AN: 152248Hom.: 20 Cov.: 32
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GnomAD3 exomes AF: 0.00193 AC: 424AN: 219172Hom.: 3 AF XY: 0.00132 AC XY: 157AN XY: 119086
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GnomAD4 exome AF: 0.000735 AC: 1048AN: 1425104Hom.: 15 Cov.: 30 AF XY: 0.000602 AC XY: 426AN XY: 707730
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GnomAD4 genome AF: 0.00767 AC: 1168AN: 152366Hom.: 20 Cov.: 32 AF XY: 0.00742 AC XY: 553AN XY: 74514
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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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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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