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GeneBe

11-27658381-T-C

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 1P and 0B. PM2_Supporting

The NM_001709.5(BDNF):c.184A>G(p.Thr62Ala) variant causes a missense change. The variant was absent in control chromosomes in GnomAD Genomes project. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Consequence

BDNF
NM_001709.5 missense

Scores

3
8
7

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 6.24

Links

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
?
Very rare variant; Number of alleles below threshold, Median coverage is 32.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
BDNFNM_001709.5 linkuse as main transcriptc.184A>G p.Thr62Ala missense_variant 2/2 ENST00000356660.9
BDNF-ASNR_033312.1 linkuse as main transcriptn.446T>C non_coding_transcript_exon_variant 4/9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
BDNFENST00000356660.9 linkuse as main transcriptc.184A>G p.Thr62Ala missense_variant 2/21 NM_001709.5 P4P23560-1
BDNF-ASENST00000651238.1 linkuse as main transcriptn.520T>C non_coding_transcript_exon_variant 5/8

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
0.00000159
AC:
1
AN:
628782
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
342534
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000286
Gnomad4 OTH exome
AF:
0.00

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsApr 07, 2022The c.184A>G (p.T62A) alteration is located in exon 1 (coding exon 1) of the BDNF gene. This alteration results from a A to G substitution at nucleotide position 184, causing the threonine (T) at amino acid position 62 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.19
BayesDel_addAF
Uncertain
0.15
D
BayesDel_noAF
Uncertain
-0.020
Cadd
Uncertain
23
Dann
Uncertain
0.99
DEOGEN2
Uncertain
0.50
D;D;.;D;D;D;D;D;D;.;D;D;D;D;D;D;.
Eigen
Uncertain
0.64
Eigen_PC
Pathogenic
0.68
FATHMM_MKL
Pathogenic
0.98
D
M_CAP
Benign
0.039
D
MetaRNN
Uncertain
0.67
D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM
Benign
-0.46
T
MutationAssessor
Uncertain
2.5
M;M;.;M;M;M;M;M;M;.;M;M;M;M;M;M;.
MutationTaster
Benign
1.0
D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
PrimateAI
Uncertain
0.56
T
PROVEAN
Benign
-0.91
N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N
REVEL
Benign
0.21
Sift
Pathogenic
0.0
D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
Sift4G
Benign
0.24
T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
Polyphen
0.96
P;P;D;P;P;P;P;P;P;D;P;P;P;P;P;P;D
Vest4
0.64
MutPred
0.28
Loss of phosphorylation at T62 (P = 0.0315);Loss of phosphorylation at T62 (P = 0.0315);.;Loss of phosphorylation at T62 (P = 0.0315);Loss of phosphorylation at T62 (P = 0.0315);Loss of phosphorylation at T62 (P = 0.0315);Loss of phosphorylation at T62 (P = 0.0315);Loss of phosphorylation at T62 (P = 0.0315);Loss of phosphorylation at T62 (P = 0.0315);.;Loss of phosphorylation at T62 (P = 0.0315);Loss of phosphorylation at T62 (P = 0.0315);Loss of phosphorylation at T62 (P = 0.0315);Loss of phosphorylation at T62 (P = 0.0315);Loss of phosphorylation at T62 (P = 0.0315);Loss of phosphorylation at T62 (P = 0.0315);.;
MVP
0.79
MPC
1.6
ClinPred
0.86
D
GERP RS
6.2
Varity_R
0.41
gMVP
0.68

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: rs1852842557; hg19: chr11-27679928; API