16-66469788-GCCACCGCCA-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_001178020.3(BEAN1):c.227_235delGCCACCACC(p.Arg76_His78del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000371 in 1,535,636 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001178020.3 disruptive_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BEAN1 | ENST00000536005.7 | c.227_235delGCCACCACC | p.Arg76_His78del | disruptive_inframe_deletion | Exon 3 of 5 | 1 | NM_001178020.3 | ENSP00000442793.2 | ||
ENSG00000260851 | ENST00000561728.1 | n.*528_*536delTGGCGGTGG | downstream_gene_variant | 2 | ENSP00000462196.1 |
Frequencies
GnomAD3 genomes AF: 0.00153 AC: 232AN: 151884Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000624 AC: 86AN: 137870Hom.: 0 AF XY: 0.000655 AC XY: 49AN XY: 74788
GnomAD4 exome AF: 0.000242 AC: 335AN: 1383634Hom.: 0 AF XY: 0.000243 AC XY: 166AN XY: 682734
GnomAD4 genome AF: 0.00154 AC: 234AN: 152002Hom.: 0 Cov.: 32 AF XY: 0.00144 AC XY: 107AN XY: 74306
ClinVar
Submissions by phenotype
BEAN1-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
BEAN1: BS1, BS2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at