chr9-92715208-G-A
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_001003800.2(BICD2):c.2514C>T(p.Thr838=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000341 in 1,612,046 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 (★).
Frequency
Genomes: 𝑓 0.000079 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000029 ( 0 hom. )
Consequence
BICD2
NM_001003800.2 synonymous
NM_001003800.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.318
Genes affected
BICD2 (HGNC:17208): (BICD cargo adaptor 2) This gene is one of two human homologs of Drosophila bicaudal-D and a member of the Bicoid family. It has been implicated in dynein-mediated, minus end-directed motility along microtubules. It has also been reported to be a phosphorylation target of NIMA related kinase 8. Two alternative splice variants have been described. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.71).
BP6
Variant 9-92715208-G-A is Benign according to our data. Variant chr9-92715208-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 705841.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.318 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0000787 (12/152384) while in subpopulation AFR AF= 0.00024 (10/41602). AF 95% confidence interval is 0.00013. There are 0 homozygotes in gnomad4. There are 3 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High AC in GnomAd4 at 12 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BICD2 | NM_001003800.2 | c.2514C>T | p.Thr838= | synonymous_variant | 7/7 | ENST00000356884.11 | |
BICD2 | NM_015250.4 | c.2469+45C>T | intron_variant | ||||
BICD2 | XM_017014551.2 | c.2550+45C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BICD2 | ENST00000356884.11 | c.2514C>T | p.Thr838= | synonymous_variant | 7/7 | 1 | NM_001003800.2 | A2 | |
BICD2 | ENST00000375512.3 | c.2469+45C>T | intron_variant | 1 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000788 AC: 12AN: 152266Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000361 AC: 9AN: 249302Hom.: 0 AF XY: 0.0000444 AC XY: 6AN XY: 135078
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GnomAD4 exome AF: 0.0000295 AC: 43AN: 1459662Hom.: 0 Cov.: 32 AF XY: 0.0000276 AC XY: 20AN XY: 725868
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GnomAD4 genome AF: 0.0000787 AC: 12AN: 152384Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74518
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Autosomal dominant childhood-onset proximal spinal muscular atrophy with contractures Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 07, 2023 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at