chr8-94393847-CA-C
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP5_Moderate
The NM_012415.3(RAD54B):c.1413del(p.Phe471LeufsTer3) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000689 in 1,450,922 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 6.9e-7 ( 0 hom. )
Consequence
RAD54B
NM_012415.3 frameshift
NM_012415.3 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.68
Genes affected
RAD54B (HGNC:17228): (RAD54 homolog B) The protein encoded by this gene belongs to the DEAD-like helicase superfamily. It shares similarity with Saccharomyces cerevisiae RAD54 and RDH54, both of which are involved in homologous recombination and repair of DNA. This protein binds to double-stranded DNA, and displays ATPase activity in the presence of DNA. This gene is highly expressed in testis and spleen, which suggests active roles in meiotic and mitotic recombination. Homozygous mutations of this gene were observed in primary lymphoma and colon cancer. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 8-94393847-CA-C is Pathogenic according to our data. Variant chr8-94393847-CA-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 870770.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RAD54B | NM_012415.3 | c.1413del | p.Phe471LeufsTer3 | frameshift_variant | 9/15 | ENST00000336148.10 | |
RAD54B | NM_001205263.2 | c.861del | p.Phe287LeufsTer3 | frameshift_variant | 7/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RAD54B | ENST00000336148.10 | c.1413del | p.Phe471LeufsTer3 | frameshift_variant | 9/15 | 1 | NM_012415.3 | P1 | |
RAD54B | ENST00000463267.5 | c.*1037del | 3_prime_UTR_variant, NMD_transcript_variant | 10/11 | 1 | ||||
RAD54B | ENST00000523192.1 | n.205del | non_coding_transcript_exon_variant | 2/2 | 2 | ||||
FSBP | ENST00000517506.2 | c.*1093del | 3_prime_UTR_variant, NMD_transcript_variant | 7/12 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome AF: 6.89e-7 AC: 1AN: 1450922Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 722226
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GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Likely pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2020 | - - |
Computational scores
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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