rs761506224
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 1P and 11B. PP2BP4BP6_ModerateBS1BS2
The NM_001003800.2(BICD2):c.485G>A(p.Arg162His) variant causes a missense change. The variant allele was found at a frequency of 0.0000167 in 1,613,556 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 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. R162C) has been classified as Likely benign.
Frequency
Consequence
NM_001003800.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BICD2 | NM_001003800.2 | c.485G>A | p.Arg162His | missense_variant | 3/7 | ENST00000356884.11 | |
BICD2 | NM_015250.4 | c.485G>A | p.Arg162His | missense_variant | 3/8 | ||
BICD2 | XM_017014551.2 | c.566G>A | p.Arg189His | missense_variant | 3/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BICD2 | ENST00000356884.11 | c.485G>A | p.Arg162His | missense_variant | 3/7 | 1 | NM_001003800.2 | A2 | |
BICD2 | ENST00000375512.3 | c.485G>A | p.Arg162His | missense_variant | 3/8 | 1 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000396 AC: 6AN: 151702Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251378Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135862
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461854Hom.: 0 Cov.: 31 AF XY: 0.0000234 AC XY: 17AN XY: 727224
GnomAD4 genome ? AF: 0.0000396 AC: 6AN: 151702Hom.: 0 Cov.: 33 AF XY: 0.0000405 AC XY: 3AN XY: 74076
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 | Dec 06, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at