13-35058893-A-T
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001385012.1(NBEA):c.1239+30A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0587 in 1,534,536 control chromosomes in the GnomAD database, including 3,036 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.046 ( 239 hom., cov: 32)
Exomes 𝑓: 0.060 ( 2797 hom. )
Consequence
NBEA
NM_001385012.1 intron
NM_001385012.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.57
Genes affected
NBEA (HGNC:7648): (neurobeachin) This gene encodes a member of a large, diverse group of A-kinase anchor proteins that target the activity of protein kinase A to specific subcellular sites by binding to its type II regulatory subunits. Brain-specific expression and coat protein-like membrane recruitment of a highly similar protein in mouse suggest an involvement in neuronal post-Golgi membrane traffic. Mutations in this gene may be associated with a form of autism. This gene and its expression are frequently disrupted in patients with multiple myeloma. Alternative splicing results in multiple transcript variants encoding distinct isoforms. Additional transcript variants may exist, but their full-length nature has not been determined.[provided by RefSeq, Feb 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0657 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NBEA | NM_001385012.1 | c.1239+30A>T | intron_variant | Intron 8 of 58 | ENST00000379939.7 | NP_001371941.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0457 AC: 6949AN: 152026Hom.: 239 Cov.: 32
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GnomAD3 exomes AF: 0.0503 AC: 9332AN: 185548Hom.: 304 AF XY: 0.0517 AC XY: 5153AN XY: 99648
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GnomAD4 exome AF: 0.0601 AC: 83101AN: 1382392Hom.: 2797 Cov.: 24 AF XY: 0.0597 AC XY: 40923AN XY: 685392
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GnomAD4 genome AF: 0.0457 AC: 6951AN: 152144Hom.: 239 Cov.: 32 AF XY: 0.0452 AC XY: 3359AN XY: 74390
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at