rs142985475
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 1P and 18B. PP2BP4_ModerateBP6_Very_StrongBS1BS2
The NM_001003800.2(BICD2):c.1481A>G(p.Gln494Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000114 in 1,611,286 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. Q494Q) 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 -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BICD2 | NM_001003800.2 | c.1481A>G | p.Gln494Arg | missense_variant | 5/7 | ENST00000356884.11 | |
BICD2 | NM_015250.4 | c.1481A>G | p.Gln494Arg | missense_variant | 5/8 | ||
BICD2 | XM_017014551.2 | c.1562A>G | p.Gln521Arg | missense_variant | 5/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BICD2 | ENST00000356884.11 | c.1481A>G | p.Gln494Arg | missense_variant | 5/7 | 1 | NM_001003800.2 | A2 | |
BICD2 | ENST00000375512.3 | c.1481A>G | p.Gln494Arg | missense_variant | 5/8 | 1 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152230Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000762 AC: 19AN: 249188Hom.: 0 AF XY: 0.0000666 AC XY: 9AN XY: 135052
GnomAD4 exome AF: 0.000120 AC: 175AN: 1458938Hom.: 0 Cov.: 32 AF XY: 0.000103 AC XY: 75AN XY: 725948
GnomAD4 genome ? AF: 0.0000525 AC: 8AN: 152348Hom.: 0 Cov.: 33 AF XY: 0.0000671 AC XY: 5AN XY: 74506
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 04, 2019 | 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
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 24, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at