chr9-92715299-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 1P and 12B. PP2BP6_Very_StrongBS2
The NM_001003800.2(BICD2):c.2423G>A(p.Arg808His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000409 in 1,612,684 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R808C) has been classified as Uncertain significance.
Frequency
Consequence
NM_001003800.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BICD2 | NM_001003800.2 | c.2423G>A | p.Arg808His | missense_variant | 7/7 | ENST00000356884.11 | |
BICD2 | NM_015250.4 | c.2423G>A | p.Arg808His | missense_variant | 7/8 | ||
BICD2 | XM_017014551.2 | c.2504G>A | p.Arg835His | missense_variant | 7/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BICD2 | ENST00000356884.11 | c.2423G>A | p.Arg808His | missense_variant | 7/7 | 1 | NM_001003800.2 | A2 | |
BICD2 | ENST00000375512.3 | c.2423G>A | p.Arg808His | missense_variant | 7/8 | 1 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000525 AC: 8AN: 152244Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000524 AC: 13AN: 248168Hom.: 0 AF XY: 0.0000519 AC XY: 7AN XY: 134912
GnomAD4 exome AF: 0.0000397 AC: 58AN: 1460440Hom.: 0 Cov.: 32 AF XY: 0.0000399 AC XY: 29AN XY: 726568
GnomAD4 genome ? AF: 0.0000525 AC: 8AN: 152244Hom.: 0 Cov.: 33 AF XY: 0.0000807 AC XY: 6AN XY: 74378
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 30, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Autosomal dominant childhood-onset proximal spinal muscular atrophy with contractures Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Apr 25, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at