16-66469788-GCCACCGCCA-GCCACCGCCACCACCGCCA
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001178020.3(BEAN1):c.227_235dupGCCACCACC(p.Arg76_His78dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000996 in 1,535,520 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000046 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00011 ( 0 hom. )
Consequence
BEAN1
NM_001178020.3 disruptive_inframe_insertion
NM_001178020.3 disruptive_inframe_insertion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.936
Genes affected
BEAN1 (HGNC:24160): (brain expressed associated with NEDD4 1) The protein encoded by this gene is one of several proteins that interact with NEDD4, a member of a family of ubiquitin-protein ligases. These proteins have PY motifs in common that bind to the WW domains of NEDD4. NEDD4 is developmentally regulated, and is highly expressed in embryonic tissues. Mutations in this gene (i.e., intronic insertions of >100 copies of pentanucleotide repeats including a (TGGAA)n sequence) are associated with spinocerebellar ataxia type 31. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2010]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BS2
High AC in GnomAd4 at 7 AD gene.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000461 AC: 7AN: 151886Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000218 AC: 3AN: 137870Hom.: 0 AF XY: 0.0000267 AC XY: 2AN XY: 74788
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GnomAD4 exome AF: 0.000106 AC: 146AN: 1383634Hom.: 0 Cov.: 32 AF XY: 0.000105 AC XY: 72AN XY: 682734
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GnomAD4 genome AF: 0.0000461 AC: 7AN: 151886Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74180
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ClinVar
Not reported inComputational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at