ENST00000299694:c.-102C>T

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2

The ENST00000299694(BEAN1):​c.-102C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000219 in 1,535,810 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.00020 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00022 ( 0 hom. )

Consequence

BEAN1
ENST00000299694 5_prime_UTR_premature_start_codon_gain

Scores

3
16

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.76
Variant links:
Genes affected
BEAN1 (HGNC:24160): (brain expressed associated with NEDD4 1) The protein encoded by this gene is one of several proteins that interact with NEDD4, a member of a family of ubiquitin-protein ligases. These proteins have PY motifs in common that bind to the WW domains of NEDD4. NEDD4 is developmentally regulated, and is highly expressed in embryonic tissues. Mutations in this gene (i.e., intronic insertions of >100 copies of pentanucleotide repeats including a (TGGAA)n sequence) are associated with spinocerebellar ataxia type 31. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2010]
BEAN1-AS1 (HGNC:51114): (BEAN1 antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.075831294).
BS2
High AC in GnomAd4 at 30 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
BEAN1NM_001178020.3 linkc.226C>T p.Arg76Cys missense_variant Exon 3 of 5 ENST00000536005.7 NP_001171491.1 Q3B7T3-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
BEAN1ENST00000536005.7 linkc.226C>T p.Arg76Cys missense_variant Exon 3 of 5 1 NM_001178020.3 ENSP00000442793.2 Q3B7T3-1
ENSG00000260851ENST00000561728.1 linkn.*523G>A downstream_gene_variant 2 ENSP00000462196.1 J3KRW8

Frequencies

GnomAD3 genomes
AF:
0.000197
AC:
30
AN:
152008
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000483
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000397
Gnomad OTH
AF:
0.000480
GnomAD3 exomes
AF:
0.000181
AC:
25
AN:
137830
Hom.:
0
AF XY:
0.000147
AC XY:
11
AN XY:
74744
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000816
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000413
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.000221
AC:
306
AN:
1383684
Hom.:
0
Cov.:
32
AF XY:
0.000224
AC XY:
153
AN XY:
682788
show subpopulations
Gnomad4 AFR exome
AF:
0.0000950
Gnomad4 AMR exome
AF:
0.0000560
Gnomad4 ASJ exome
AF:
0.0000795
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000269
Gnomad4 OTH exome
AF:
0.000138
GnomAD4 genome
AF:
0.000197
AC:
30
AN:
152126
Hom.:
0
Cov.:
32
AF XY:
0.000202
AC XY:
15
AN XY:
74370
show subpopulations
Gnomad4 AFR
AF:
0.0000482
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000397
Gnomad4 OTH
AF:
0.000475
Alfa
AF:
0.000217
Hom.:
0
Bravo
AF:
0.000170
TwinsUK
AF:
0.000270
AC:
1
ALSPAC
AF:
0.000259
AC:
1
ExAC
AF:
0.000103
AC:
6

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.16
BayesDel_addAF
Benign
-0.15
T
BayesDel_noAF
Benign
-0.45
CADD
Benign
22
DANN
Uncertain
1.0
DEOGEN2
Benign
0.024
T
Eigen
Benign
-0.23
Eigen_PC
Benign
-0.23
FATHMM_MKL
Benign
0.21
N
LIST_S2
Benign
0.68
T
M_CAP
Uncertain
0.11
D
MetaRNN
Benign
0.076
T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.0
N
PrimateAI
Benign
0.35
T
PROVEAN
Benign
-1.5
N
REVEL
Benign
0.076
Sift
Uncertain
0.022
D
Sift4G
Benign
0.14
T
Vest4
0.34
MVP
0.47
ClinPred
0.21
T
GERP RS
4.1
Varity_R
0.12
gMVP
0.17

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: rs200706119; hg19: chr16-66503705; API