chr13-42964145-G-GA
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_033255.5(EPSTI1):c.332-7_332-6insT variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00464 in 1,589,758 control chromosomes in the GnomAD database, including 237 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.023 ( 139 hom., cov: 32)
Exomes 𝑓: 0.0027 ( 98 hom. )
Consequence
EPSTI1
NM_033255.5 splice_region, splice_polypyrimidine_tract, intron
NM_033255.5 splice_region, splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.206
Genes affected
EPSTI1 (HGNC:16465): (epithelial stromal interaction 1) The protein encoded by this gene has been shown to promote tumor invasion and metastasis in some invasive cancer cells when overexpressed. Expression of this gene has been shown to be upregulated by direct binding of the Kruppel like factor 8 protein to promoter sequences. The translated protein interacts with the amino terminal region of the valosin containing protein gene product, resulting in the nuclear translocation of the nuclear factor kappa B subunit 1 gene product, and activation of target genes. Overexpression of this gene has been observed in some breast cancers and in some individuals with systemic lupus erythematosus (SLE). [provided by RefSeq, Sep 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 13-42964145-G-GA is Benign according to our data. Variant chr13-42964145-G-GA is described in ClinVar as [Benign]. Clinvar id is 784269.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0797 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EPSTI1 | NM_033255.5 | c.332-7_332-6insT | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000313624.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EPSTI1 | ENST00000313624.12 | c.332-7_332-6insT | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_033255.5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0234 AC: 3516AN: 150084Hom.: 137 Cov.: 32
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GnomAD3 exomes AF: 0.00688 AC: 1540AN: 223988Hom.: 45 AF XY: 0.00492 AC XY: 597AN XY: 121344
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GnomAD4 exome AF: 0.00268 AC: 3851AN: 1439560Hom.: 98 Cov.: 29 AF XY: 0.00235 AC XY: 1681AN XY: 716180
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GnomAD4 genome ? AF: 0.0235 AC: 3526AN: 150198Hom.: 139 Cov.: 32 AF XY: 0.0229 AC XY: 1681AN XY: 73288
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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 | Apr 10, 2018 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at