11-27658200-A-G
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001709.5(BDNF):āc.365T>Cā(p.Met122Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000477 in 1,614,020 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Genomes: š 0.000013 ( 0 hom., cov: 32)
Exomes š: 0.000051 ( 0 hom. )
Consequence
BDNF
NM_001709.5 missense
NM_001709.5 missense
Scores
7
4
8
Clinical Significance
Conservation
PhyloP100: 9.32
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 made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BS2
High AC in GnomAdExome4 at 75 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BDNF | NM_001709.5 | c.365T>C | p.Met122Thr | missense_variant | 2/2 | ENST00000356660.9 | NP_001700.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152082Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000116 AC: 29AN: 250896Hom.: 0 AF XY: 0.000155 AC XY: 21AN XY: 135666
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GnomAD4 exome AF: 0.0000513 AC: 75AN: 1461820Hom.: 0 Cov.: 32 AF XY: 0.0000825 AC XY: 60AN XY: 727208
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GnomAD4 genome AF: 0.0000131 AC: 2AN: 152200Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74412
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
BDNF-related disorder Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 05, 2024 | The BDNF c.611T>C variant is predicted to result in the amino acid substitution p.Met204Thr. This variant has been reported in the homozygous state in an individual with intellectual disability (referred to as c.365T>C, p.Met122Thr in table 2, Harripaul et al. 2017. PubMed ID: 28397838). This variant is reported in 0.095% of alleles in individuals of South Asian descent in gnomAD. Although we suspect that this variant may be benign, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Pathogenic
CADD
Uncertain
DANN
Benign
DEOGEN2
Benign
T;T;.;T;T;T;T;T;T;.;T;T;T;T;T;T;.
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
.;.;D;.;.;.;.;.;.;D;D;.;.;.;.;.;D
M_CAP
Benign
D
MetaRNN
Uncertain
T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;N;.;N;N;N;N;N;N;.;N;N;N;N;N;N;.
PrimateAI
Pathogenic
D
PROVEAN
Benign
N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N
REVEL
Uncertain
Sift
Pathogenic
D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
Sift4G
Uncertain
T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
Polyphen
P;P;P;P;P;P;P;P;P;D;P;P;P;P;P;P;P
Vest4
MutPred
Gain of phosphorylation at M122 (P = 0.0739);Gain of phosphorylation at M122 (P = 0.0739);.;Gain of phosphorylation at M122 (P = 0.0739);Gain of phosphorylation at M122 (P = 0.0739);Gain of phosphorylation at M122 (P = 0.0739);Gain of phosphorylation at M122 (P = 0.0739);Gain of phosphorylation at M122 (P = 0.0739);Gain of phosphorylation at M122 (P = 0.0739);.;Gain of phosphorylation at M122 (P = 0.0739);Gain of phosphorylation at M122 (P = 0.0739);Gain of phosphorylation at M122 (P = 0.0739);Gain of phosphorylation at M122 (P = 0.0739);Gain of phosphorylation at M122 (P = 0.0739);Gain of phosphorylation at M122 (P = 0.0739);.;
MVP
MPC
1.5
ClinPred
T
GERP RS
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gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at