rs556905704
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP6_ModerateBS2
The NM_001003800.2(BICD2):c.2429G>A(p.Arg810His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000316 in 1,612,556 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. R810C) 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 Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BICD2 | NM_001003800.2 | c.2429G>A | p.Arg810His | missense_variant | 7/7 | ENST00000356884.11 | |
BICD2 | NM_015250.4 | c.2429G>A | p.Arg810His | missense_variant | 7/8 | ||
BICD2 | XM_017014551.2 | c.2510G>A | p.Arg837His | missense_variant | 7/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BICD2 | ENST00000356884.11 | c.2429G>A | p.Arg810His | missense_variant | 7/7 | 1 | NM_001003800.2 | A2 | |
BICD2 | ENST00000375512.3 | c.2429G>A | p.Arg810His | missense_variant | 7/8 | 1 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000657 AC: 10AN: 152204Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000202 AC: 5AN: 247538Hom.: 0 AF XY: 0.00000742 AC XY: 1AN XY: 134702
GnomAD4 exome AF: 0.0000281 AC: 41AN: 1460352Hom.: 0 Cov.: 32 AF XY: 0.0000151 AC XY: 11AN XY: 726518
GnomAD4 genome ? AF: 0.0000657 AC: 10AN: 152204Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74354
ClinVar
Submissions by phenotype
Autosomal dominant childhood-onset proximal spinal muscular atrophy with contractures Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 19, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at