rs151133287
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001003800.2(BICD2):c.2397C>T(p.Leu799=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000639 in 1,612,950 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts 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. L799L) has been classified as Likely benign.
Frequency
Consequence
NM_001003800.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BICD2 | NM_001003800.2 | c.2397C>T | p.Leu799= | synonymous_variant | 7/7 | ENST00000356884.11 | |
BICD2 | NM_015250.4 | c.2397C>T | p.Leu799= | synonymous_variant | 7/8 | ||
BICD2 | XM_017014551.2 | c.2478C>T | p.Leu826= | synonymous_variant | 7/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BICD2 | ENST00000356884.11 | c.2397C>T | p.Leu799= | synonymous_variant | 7/7 | 1 | NM_001003800.2 | A2 | |
BICD2 | ENST00000375512.3 | c.2397C>T | p.Leu799= | synonymous_variant | 7/8 | 1 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000591 AC: 90AN: 152256Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000631 AC: 157AN: 248692Hom.: 0 AF XY: 0.000607 AC XY: 82AN XY: 135102
GnomAD4 exome AF: 0.000644 AC: 940AN: 1460576Hom.: 1 Cov.: 32 AF XY: 0.000663 AC XY: 482AN XY: 726632
GnomAD4 genome ? AF: 0.000591 AC: 90AN: 152374Hom.: 0 Cov.: 33 AF XY: 0.000537 AC XY: 40AN XY: 74508
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 13, 2020 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2022 | BICD2: BP4, BP7 - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 11, 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 | Dec 26, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at