2-241189032-G-A
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001370694.2(ANO7):c.-8+266G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 152,142 control chromosomes in the GnomAD database, including 10,663 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.35 ( 10663 hom., cov: 33)
Consequence
ANO7
NM_001370694.2 intron
NM_001370694.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.215
Genes affected
ANO7 (HGNC:31677): (anoctamin 7) This prostate-specific gene encodes a cytoplasmic protein, as well as a polytopic membrane protein which may serve as a target in prostate cancer diagnosis and immunotherapy. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Aug 2011]
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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=-0.9).
BP6
Variant 2-241189032-G-A is Benign according to our data. Variant chr2-241189032-G-A is described in ClinVar as [Benign]. Clinvar id is 1247216.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANO7 | NM_001370694.2 | c.-8+266G>A | intron_variant | ENST00000674324.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANO7 | ENST00000674324.2 | c.-8+266G>A | intron_variant | NM_001370694.2 | A2 | ||||
ANO7 | ENST00000274979.12 | c.155+266G>A | intron_variant | 1 | P2 | ||||
ANO7 | ENST00000402530.8 | c.-8+266G>A | intron_variant | 1 | |||||
ANO7 | ENST00000402430.8 | c.-8+266G>A | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.350 AC: 53133AN: 152024Hom.: 10671 Cov.: 33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.349 AC: 53116AN: 152142Hom.: 10663 Cov.: 33 AF XY: 0.344 AC XY: 25565AN XY: 74400
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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 | GeneDx | Jun 18, 2021 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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