rs998616675
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM4BS2
The NM_001003800.2(BICD2):c.1704_1721delTCCCGGGGGCCGCACCAG(p.Pro569_Ser574del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.0000056 in 1,607,506 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000048 ( 0 hom. )
Consequence
BICD2
NM_001003800.2 disruptive_inframe_deletion
NM_001003800.2 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 5.84
Publications
0 publications found
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]
BICD2 Gene-Disease associations (from GenCC):
- autosomal dominant childhood-onset proximal spinal muscular atrophy with contracturesInheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Genomics England PanelApp, G2P, Ambry Genetics, Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM4
Nonframeshift variant in NON repetitive region in NM_001003800.2.
BS2
High AC in GnomAdExome4 at 7 AD gene.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001003800.2. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| BICD2 | MANE Select | c.1704_1721delTCCCGGGGGCCGCACCAG | p.Pro569_Ser574del | disruptive_inframe_deletion | Exon 5 of 7 | NP_001003800.1 | Q8TD16-2 | ||
| BICD2 | c.1704_1721delTCCCGGGGGCCGCACCAG | p.Pro569_Ser574del | disruptive_inframe_deletion | Exon 5 of 8 | NP_056065.1 | Q8TD16-1 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| BICD2 | TSL:1 MANE Select | c.1704_1721delTCCCGGGGGCCGCACCAG | p.Pro569_Ser574del | disruptive_inframe_deletion | Exon 5 of 7 | ENSP00000349351.6 | Q8TD16-2 | ||
| BICD2 | TSL:1 | c.1704_1721delTCCCGGGGGCCGCACCAG | p.Pro569_Ser574del | disruptive_inframe_deletion | Exon 5 of 8 | ENSP00000364662.3 | Q8TD16-1 |
Frequencies
GnomAD3 genomes 0.0000131 AC: 2AN: 152164Hom.: 0 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
2
AN:
152164
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.00000481 AC: 7AN: 1455342Hom.: 0 AF XY: 0.00000829 AC XY: 6AN XY: 723912 show subpopulations
GnomAD4 exome
AF:
AC:
7
AN:
1455342
Hom.:
AF XY:
AC XY:
6
AN XY:
723912
show subpopulations
African (AFR)
AF:
AC:
1
AN:
33376
American (AMR)
AF:
AC:
0
AN:
44506
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26014
East Asian (EAS)
AF:
AC:
0
AN:
39650
South Asian (SAS)
AF:
AC:
0
AN:
86030
European-Finnish (FIN)
AF:
AC:
0
AN:
49956
Middle Eastern (MID)
AF:
AC:
0
AN:
4942
European-Non Finnish (NFE)
AF:
AC:
5
AN:
1110738
Other (OTH)
AF:
AC:
1
AN:
60130
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.468
Heterozygous variant carriers
0
1
2
2
3
4
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
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8
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<30
30-35
35-40
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Age
GnomAD4 genome 0.0000131 AC: 2AN: 152164Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74324 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
GnomAD4 genome
AF:
AC:
2
AN:
152164
Hom.:
Cov.:
33
AF XY:
AC XY:
1
AN XY:
74324
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
41436
American (AMR)
AF:
AC:
2
AN:
15286
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3468
East Asian (EAS)
AF:
AC:
0
AN:
5172
South Asian (SAS)
AF:
AC:
0
AN:
4838
European-Finnish (FIN)
AF:
AC:
0
AN:
10622
Middle Eastern (MID)
AF:
AC:
0
AN:
314
European-Non Finnish (NFE)
AF:
AC:
0
AN:
68022
Other (OTH)
AF:
AC:
0
AN:
2094
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.00233887), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.350
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
Autosomal dominant childhood-onset proximal spinal muscular atrophy with contractures (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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