chr11-27658115-C-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The ENST00000356660.9(BDNF):c.450G>A(p.Ala150Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000633 in 1,614,124 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0034 ( 2 hom., cov: 32)
Exomes 𝑓: 0.00035 ( 5 hom. )
Consequence
BDNF
ENST00000356660.9 synonymous
ENST00000356660.9 synonymous
Scores
1
Clinical Significance
Conservation
PhyloP100: -2.00
Publications
21 publications found
Genes affected
BDNF (HGNC:1033): (brain derived neurotrophic factor) This gene encodes a member of the nerve growth factor family of proteins. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein that is proteolytically processed to generate the mature protein. Binding of this protein to its cognate receptor promotes neuronal survival in the adult brain. Expression of this gene is reduced in Alzheimer's, Parkinson's, and Huntington's disease patients. This gene may play a role in the regulation of the stress response and in the biology of mood disorders. [provided by RefSeq, Nov 2015]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -17 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.62).
BP6
Variant 11-27658115-C-T is Benign according to our data. Variant chr11-27658115-C-T is described in ClinVar as Benign. ClinVar VariationId is 783114.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-2 with no splicing effect.
BS2
High AC in GnomAd4 at 517 AD gene.
Variant Effect in Transcripts
ACMG analysis was done for transcript: ENST00000356660.9. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| BDNF | NM_001709.5 | MANE Select | c.450G>A | p.Ala150Ala | synonymous | Exon 2 of 2 | NP_001700.2 | ||
| BDNF | NM_001143810.2 | c.696G>A | p.Ala232Ala | synonymous | Exon 3 of 3 | NP_001137282.1 | |||
| BDNF | NM_001143809.2 | c.537G>A | p.Ala179Ala | synonymous | Exon 2 of 2 | NP_001137281.1 |
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| BDNF | ENST00000356660.9 | TSL:1 MANE Select | c.450G>A | p.Ala150Ala | synonymous | Exon 2 of 2 | ENSP00000349084.4 | ||
| BDNF | ENST00000438929.5 | TSL:1 | c.696G>A | p.Ala232Ala | synonymous | Exon 3 of 3 | ENSP00000414303.1 | ||
| BDNF | ENST00000395986.6 | TSL:1 | c.495G>A | p.Ala165Ala | synonymous | Exon 2 of 2 | ENSP00000379309.2 |
Frequencies
GnomAD3 genomes 0.00340 AC: 517AN: 152116Hom.: 2 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
517
AN:
152116
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:
GnomAD4 exome AF: 0.000345 AC: 505AN: 1461890Hom.: 5 Cov.: 32 AF XY: 0.000289 AC XY: 210AN XY: 727246 show subpopulations
GnomAD4 exome
AF:
AC:
505
AN:
1461890
Hom.:
Cov.:
32
AF XY:
AC XY:
210
AN XY:
727246
show subpopulations
African (AFR)
AF:
AC:
413
AN:
33480
American (AMR)
AF:
AC:
33
AN:
44724
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26136
East Asian (EAS)
AF:
AC:
2
AN:
39700
South Asian (SAS)
AF:
AC:
2
AN:
86258
European-Finnish (FIN)
AF:
AC:
0
AN:
53416
Middle Eastern (MID)
AF:
AC:
2
AN:
5768
European-Non Finnish (NFE)
AF:
AC:
16
AN:
1112012
Other (OTH)
AF:
AC:
37
AN:
60396
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.511
Heterozygous variant carriers
0
42
84
127
169
211
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
20
40
60
80
100
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome 0.00340 AC: 517AN: 152234Hom.: 2 Cov.: 32 AF XY: 0.00331 AC XY: 246AN XY: 74424 show subpopulations
GnomAD4 genome
AF:
AC:
517
AN:
152234
Hom.:
Cov.:
32
AF XY:
AC XY:
246
AN XY:
74424
show subpopulations
African (AFR)
AF:
AC:
490
AN:
41528
American (AMR)
AF:
AC:
19
AN:
15298
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3470
East Asian (EAS)
AF:
AC:
0
AN:
5172
South Asian (SAS)
AF:
AC:
0
AN:
4820
European-Finnish (FIN)
AF:
AC:
0
AN:
10608
Middle Eastern (MID)
AF:
AC:
0
AN:
294
European-Non Finnish (NFE)
AF:
AC:
1
AN:
68022
Other (OTH)
AF:
AC:
7
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
31
61
92
122
153
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Variant carriers
0
10
20
30
40
50
<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:
ClinVar
ClinVar submissions as Germline
Significance:Benign
Revision:criteria provided, multiple submitters, no conflicts
Pathogenic
VUS
Benign
Condition
-
-
1
not provided (1)
-
-
1
not specified (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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