rs3866958
Positions:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The ENST00000674596.1(B9D1):c.-129+166T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.927 in 260,162 control chromosomes in the GnomAD database, including 113,251 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.89 ( 61414 hom., cov: 33)
Exomes 𝑓: 0.98 ( 51837 hom. )
Consequence
B9D1
ENST00000674596.1 intron
ENST00000674596.1 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.34
Genes affected
B9D1 (HGNC:24123): (B9 domain containing 1) This gene encodes a B9 domain-containing protein, one of several that are involved in ciliogenesis. Alterations in expression of this gene have been found in a family with Meckel syndrome. Meckel syndrome has been associated with at least six different genes. This gene is located within the Smith-Magenis syndrome region on chromosome 17. [provided by RefSeq, Mar 2016]
MAPK7 (HGNC:6880): (mitogen-activated protein kinase 7) The protein encoded by this gene is a member of the MAP kinase family. MAP kinases act as an integration point for multiple biochemical signals, and are involved in a wide variety of cellular processes such as proliferation, differentiation, transcription regulation and development. This kinase is specifically activated by mitogen-activated protein kinase kinase 5 (MAP2K5/MEK5). It is involved in the downstream signaling processes of various receptor molecules including receptor type kinases, and G protein-coupled receptors. In response to extracelluar signals, this kinase translocates to cell nucleus, where it regulates gene expression by phosphorylating, and activating different transcription factors. Four alternatively spliced transcript variants of this gene encoding two distinct isoforms have been reported. [provided by RefSeq, Jul 2008]
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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=-0.84).
BP6
?
Variant 17-19377693-A-C is Benign according to our data. Variant chr17-19377693-A-C is described in ClinVar as [Benign]. Clinvar id is 1178285.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.981 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
B9D1 | NM_001368769.2 | c.-298+166T>G | intron_variant | ||||
B9D1 | XM_005256610.3 | c.-1456+166T>G | intron_variant | ||||
B9D1 | XM_047435750.1 | c.-96+166T>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
B9D1 | ENST00000477478.7 | c.-298+166T>G | intron_variant | 3 | |||||
B9D1 | ENST00000582857.2 | c.-298+166T>G | intron_variant | 4 | |||||
B9D1 | ENST00000642870.2 | c.-298+166T>G | intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.890 AC: 135425AN: 152118Hom.: 61371 Cov.: 33
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GnomAD4 exome AF: 0.979 AC: 105617AN: 107926Hom.: 51837 Cov.: 4 AF XY: 0.979 AC XY: 50549AN XY: 51616
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GnomAD4 genome ? AF: 0.890 AC: 135524AN: 152236Hom.: 61414 Cov.: 33 AF XY: 0.887 AC XY: 66010AN XY: 74434
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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 | Jan 28, 2020 | This variant is associated with the following publications: (PMID: 23804708) - |
Computational scores
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Name
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at