rs1800820
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PVS1_StrongPM2
The NM_030578.4(B9D2):c.358C>T(p.Arg120Ter) variant causes a stop gained change. The variant allele was found at a frequency of 0.00000682 in 1,613,740 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000055 ( 0 hom. )
Consequence
B9D2
NM_030578.4 stop_gained
NM_030578.4 stop_gained
Scores
2
3
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 4.06
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 Likely_pathogenic. Variant got 6 ACMG points.
PVS1
?
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. Fraction of 0.322 CDS is truncated, and there are 1 pathogenic variants in the truncated region.
PM2
?
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
B9D2 | NM_030578.4 | c.358C>T | p.Arg120Ter | stop_gained | 4/4 | ENST00000243578.8 | |
B9D2 | XM_011527349.3 | c.358C>T | p.Arg120Ter | stop_gained | 4/4 | ||
B9D2 | XM_011527350.3 | c.199C>T | p.Arg67Ter | stop_gained | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
B9D2 | ENST00000243578.8 | c.358C>T | p.Arg120Ter | stop_gained | 4/4 | 1 | NM_030578.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152216Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000161 AC: 4AN: 248330Hom.: 0 AF XY: 0.00000742 AC XY: 1AN XY: 134716
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GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461524Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 4AN XY: 727068
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
Cadd
Pathogenic
Dann
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Uncertain
FATHMM_MKL
Benign
D
MutationTaster
Benign
D;D
Vest4
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at