chr8-94387323-A-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_012415.3(RAD54B):c.1810-164T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.501 in 556,168 control chromosomes in the GnomAD database, including 75,488 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.45 ( 17188 hom., cov: 30)
Exomes 𝑓: 0.52 ( 58300 hom. )
Consequence
RAD54B
NM_012415.3 intron
NM_012415.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.438
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 Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BP6
?
Variant 8-94387323-A-T is Benign according to our data. Variant chr8-94387323-A-T is described in ClinVar as [Benign]. Clinvar id is 1267064.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.58 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RAD54B | NM_012415.3 | c.1810-164T>A | intron_variant | ENST00000336148.10 | |||
RAD54B | NM_001205263.2 | c.1258-164T>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RAD54B | ENST00000336148.10 | c.1810-164T>A | intron_variant | 1 | NM_012415.3 | P1 | |||
RAD54B | ENST00000518358.1 | n.107T>A | non_coding_transcript_exon_variant | 1/2 | 3 | ||||
FSBP | ENST00000517506.2 | c.*1490-164T>A | intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.449 AC: 68166AN: 151724Hom.: 17186 Cov.: 30
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GnomAD4 exome AF: 0.520 AC: 210174AN: 404326Hom.: 58300 Cov.: 5 AF XY: 0.518 AC XY: 109265AN XY: 210770
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GnomAD4 genome ? AF: 0.449 AC: 68199AN: 151842Hom.: 17188 Cov.: 30 AF XY: 0.444 AC XY: 32982AN XY: 74212
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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 | Nov 12, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at