rs1800468
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_030578.4(B9D2):c.*18G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0753 in 1,613,668 control chromosomes in the GnomAD database, including 5,061 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.059 ( 319 hom., cov: 32)
Exomes 𝑓: 0.077 ( 4742 hom. )
Consequence
B9D2
NM_030578.4 3_prime_UTR
NM_030578.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.133
Genes affected
B9D2 (HGNC:28636): (B9 domain containing 2) This gene encodes a B9 domain protein, which are exclusively found in ciliated organisms. The gene is upregulated during mucociliary differentiation, and the encoded protein localizes to basal bodies and cilia. Disrupting expression of this gene results in ciliogenesis defects. [provided by RefSeq, Oct 2009]
TMEM91 (HGNC:32393): (transmembrane protein 91) Predicted to act upstream of or within hematopoietic progenitor cell differentiation. Predicted to be integral component of membrane. Predicted to be active in intracellular membrane-bounded organelle and membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BP6
?
Variant 19-41354682-C-T is Benign according to our data. Variant chr19-41354682-C-T is described in ClinVar as [Benign]. Clinvar id is 261879.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-41354682-C-T is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0792 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
B9D2 | NM_030578.4 | c.*18G>A | 3_prime_UTR_variant | 4/4 | ENST00000243578.8 | ||
B9D2 | XM_011527349.3 | c.*18G>A | 3_prime_UTR_variant | 4/4 | |||
B9D2 | XM_011527350.3 | c.*18G>A | 3_prime_UTR_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
B9D2 | ENST00000243578.8 | c.*18G>A | 3_prime_UTR_variant | 4/4 | 1 | NM_030578.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0592 AC: 8998AN: 152088Hom.: 319 Cov.: 32
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GnomAD3 exomes AF: 0.0622 AC: 15532AN: 249712Hom.: 567 AF XY: 0.0642 AC XY: 8681AN XY: 135236
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GnomAD4 exome AF: 0.0770 AC: 112467AN: 1461462Hom.: 4742 Cov.: 32 AF XY: 0.0772 AC XY: 56119AN XY: 727032
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GnomAD4 genome ? AF: 0.0591 AC: 9000AN: 152206Hom.: 319 Cov.: 32 AF XY: 0.0578 AC XY: 4303AN XY: 74406
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Meckel-Gruber syndrome;C0431399:Familial aplasia of the vermis Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Sep 11, 2023 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 09, 2018 | This variant is associated with the following publications: (PMID: 9887336) - |
Meckel syndrome, type 10 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 14, 2021 | - - |
Computational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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