13-35058893-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001385012.1(NBEA):​c.1239+30A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0587 in 1,534,536 control chromosomes in the GnomAD database, including 3,036 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 0.046 ( 239 hom., cov: 32)
Exomes 𝑓: 0.060 ( 2797 hom. )

Consequence

NBEA
NM_001385012.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.57
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0657 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NBEANM_001385012.1 linkc.1239+30A>T intron_variant Intron 8 of 58 ENST00000379939.7 NP_001371941.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NBEAENST00000379939.7 linkc.1239+30A>T intron_variant Intron 8 of 58 5 NM_001385012.1 ENSP00000369271.2 Q5T321

Frequencies

GnomAD3 genomes
AF:
0.0457
AC:
6949
AN:
152026
Hom.:
239
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0113
Gnomad AMI
AF:
0.181
Gnomad AMR
AF:
0.0307
Gnomad ASJ
AF:
0.0681
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.0441
Gnomad FIN
AF:
0.0675
Gnomad MID
AF:
0.0411
Gnomad NFE
AF:
0.0673
Gnomad OTH
AF:
0.0446
GnomAD3 exomes
AF:
0.0503
AC:
9332
AN:
185548
Hom.:
304
AF XY:
0.0517
AC XY:
5153
AN XY:
99648
show subpopulations
Gnomad AFR exome
AF:
0.0121
Gnomad AMR exome
AF:
0.0196
Gnomad ASJ exome
AF:
0.0644
Gnomad EAS exome
AF:
0.000222
Gnomad SAS exome
AF:
0.0517
Gnomad FIN exome
AF:
0.0659
Gnomad NFE exome
AF:
0.0677
Gnomad OTH exome
AF:
0.0526
GnomAD4 exome
AF:
0.0601
AC:
83101
AN:
1382392
Hom.:
2797
Cov.:
24
AF XY:
0.0597
AC XY:
40923
AN XY:
685392
show subpopulations
Gnomad4 AFR exome
AF:
0.0100
Gnomad4 AMR exome
AF:
0.0213
Gnomad4 ASJ exome
AF:
0.0639
Gnomad4 EAS exome
AF:
0.000241
Gnomad4 SAS exome
AF:
0.0489
Gnomad4 FIN exome
AF:
0.0647
Gnomad4 NFE exome
AF:
0.0659
Gnomad4 OTH exome
AF:
0.0543
GnomAD4 genome
AF:
0.0457
AC:
6951
AN:
152144
Hom.:
239
Cov.:
32
AF XY:
0.0452
AC XY:
3359
AN XY:
74390
show subpopulations
Gnomad4 AFR
AF:
0.0113
Gnomad4 AMR
AF:
0.0307
Gnomad4 ASJ
AF:
0.0681
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.0446
Gnomad4 FIN
AF:
0.0675
Gnomad4 NFE
AF:
0.0673
Gnomad4 OTH
AF:
0.0441
Alfa
AF:
0.0281
Hom.:
22
Bravo
AF:
0.0406
Asia WGS
AF:
0.0130
AC:
45
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.0070
DANN
Benign
0.73

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs17775456; hg19: chr13-35633030; API