GeneBe

16-66480766-G-T

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7

The NM_001178020.3(BEAN1):​c.621G>T​(p.Thr207Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. T207T) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

BEAN1
NM_001178020.3 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.825

Publications

0 publications found
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)

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP7
Synonymous conserved (PhyloP=-0.825 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001178020.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
BEAN1
NM_001178020.3
MANE Select
c.621G>Tp.Thr207Thr
synonymous
Exon 5 of 5NP_001171491.1Q3B7T3-1
BEAN1
NM_001136106.5
c.294G>Tp.Thr98Thr
synonymous
Exon 4 of 4NP_001129578.1Q3B7T3-2
BEAN1
NM_001197224.4
c.114-2112G>T
intron
N/ANP_001184153.1

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
BEAN1
ENST00000536005.7
TSL:1 MANE Select
c.621G>Tp.Thr207Thr
synonymous
Exon 5 of 5ENSP00000442793.2Q3B7T3-1
BEAN1
ENST00000299694.12
TSL:1
c.294G>Tp.Thr98Thr
synonymous
Exon 4 of 4ENSP00000299694.8Q3B7T3-2
ENSG00000260851
ENST00000561728.1
TSL:2
n.*11+398C>A
intron
N/AENSP00000462196.1J3KRW8

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1398966
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
690016
African (AFR)
AF:
0.00
AC:
0
AN:
31590
American (AMR)
AF:
0.00
AC:
0
AN:
35674
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
25152
East Asian (EAS)
AF:
0.00
AC:
0
AN:
35734
South Asian (SAS)
AF:
0.00
AC:
0
AN:
79206
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
49066
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5690
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
1078864
Other (OTH)
AF:
0.00
AC:
0
AN:
57990
GnomAD4 genome
Cov.:
33
Alfa
AF:
0.0000256
Hom.:
0
Bravo
AF:
0.0000113

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
CADD
Benign
1.1
DANN
Benign
0.86
PhyloP100
-0.82

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

Other links and lift over

dbSNP: rs755130190; hg19: chr16-66514669; API