chr13-35194652-C-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001385012.1(NBEA):c.4928-1212C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 151,910 control chromosomes in the GnomAD database, including 1,508 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.13 ( 1508 hom., cov: 32)
Consequence
NBEA
NM_001385012.1 intron
NM_001385012.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.105
Publications
4 publications found
Genes affected
NBEA (HGNC:7648): (neurobeachin) This gene encodes a member of a large, diverse group of A-kinase anchor proteins that target the activity of protein kinase A to specific subcellular sites by binding to its type II regulatory subunits. Brain-specific expression and coat protein-like membrane recruitment of a highly similar protein in mouse suggest an involvement in neuronal post-Golgi membrane traffic. Mutations in this gene may be associated with a form of autism. This gene and its expression are frequently disrupted in patients with multiple myeloma. Alternative splicing results in multiple transcript variants encoding distinct isoforms. Additional transcript variants may exist, but their full-length nature has not been determined.[provided by RefSeq, Feb 2011]
NBEA Gene-Disease associations (from GenCC):
- complex neurodevelopmental disorderInheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
- neurodevelopmental disorder with or without early-onset generalized epilepsyInheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
- syndromic intellectual disabilityInheritance: AD Classification: STRONG Submitted by: Illumina
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.01).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NBEA | NM_001385012.1 | c.4928-1212C>T | intron_variant | Intron 30 of 58 | ENST00000379939.7 | NP_001371941.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.130 AC: 19777AN: 151792Hom.: 1506 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
19777
AN:
151792
Hom.:
Cov.:
32
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.130 AC: 19807AN: 151910Hom.: 1508 Cov.: 32 AF XY: 0.132 AC XY: 9783AN XY: 74228 show subpopulations
GnomAD4 genome
AF:
AC:
19807
AN:
151910
Hom.:
Cov.:
32
AF XY:
AC XY:
9783
AN XY:
74228
show subpopulations
African (AFR)
AF:
AC:
8270
AN:
41462
American (AMR)
AF:
AC:
1115
AN:
15268
Ashkenazi Jewish (ASJ)
AF:
AC:
337
AN:
3466
East Asian (EAS)
AF:
AC:
330
AN:
5158
South Asian (SAS)
AF:
AC:
878
AN:
4812
European-Finnish (FIN)
AF:
AC:
1499
AN:
10516
Middle Eastern (MID)
AF:
AC:
27
AN:
294
European-Non Finnish (NFE)
AF:
AC:
6976
AN:
67916
Other (OTH)
AF:
AC:
243
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
831
1662
2493
3324
4155
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
230
460
690
920
1150
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
440
AN:
3452
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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