11-27657906-A-G

Position:

• chr11-27657906-A-G

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2 PP3

The NM_001709.5(BDNF):​c.659T>C​(p.Met220Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: BDNF NM_001709.5 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 7.51

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]

BDNF-AS (HGNC:20608): (BDNF antisense RNA)

ACMG classification

Verdict is Uncertain_significance. Variant got 3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.815

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BDNF	NM_001709.5	c.659T>C	p.Met220Thr	missense_variant	2/2	ENST00000356660.9
BDNF-AS	NR_033312.1	n.306-335A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BDNF	ENST00000356660.9	c.659T>C	p.Met220Thr	missense_variant	2/2	1	NM_001709.5	P4
BDNF-AS	ENST00000651238.1	n.380-335A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

BDNF-related disorder Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Jan 26, 2023

The BDNF c.905T>C variant is predicted to result in the amino acid substitution p.Met302Thr. To our knowledge, this variant has not been reported in the literature or in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.44
BayesDel_addAF	Pathogenic	0.30	D
BayesDel_noAF	Pathogenic	0.20
CADD	Uncertain	25
DANN	Benign	0.88
DEOGEN2	Uncertain	0.48	T;T;.;T;T;T;T;T;T;.;T;T;T;T;T;T;.
Eigen	Uncertain	0.31
Eigen_PC	Uncertain	0.47
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Benign	0.79	.;.;T;.;.;.;.;.;.;T;T;.;.;.;.;.;T
M_CAP	Benign	0.061	D
MetaRNN	Pathogenic	0.82	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM	Benign	-0.52	T
MutationAssessor	Benign	1.4	L;L;.;L;L;L;L;L;L;.;L;L;L;L;L;L;.
MutationTaster	Benign	1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
PrimateAI	Pathogenic	0.89	D
PROVEAN	Benign	-2.3	N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N
REVEL	Uncertain	0.52
Sift	Uncertain	0.011	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
Sift4G	Benign	0.37	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
Polyphen		0.23	B;B;B;B;B;B;B;B;B;P;B;B;B;B;B;B;B
Vest4		0.80
MutPred		0.67		Gain of phosphorylation at M220 (P = 0.0288);Gain of phosphorylation at M220 (P = 0.0288);.;Gain of phosphorylation at M220 (P = 0.0288);Gain of phosphorylation at M220 (P = 0.0288);Gain of phosphorylation at M220 (P = 0.0288);Gain of phosphorylation at M220 (P = 0.0288);Gain of phosphorylation at M220 (P = 0.0288);Gain of phosphorylation at M220 (P = 0.0288);.;Gain of phosphorylation at M220 (P = 0.0288);Gain of phosphorylation at M220 (P = 0.0288);Gain of phosphorylation at M220 (P = 0.0288);Gain of phosphorylation at M220 (P = 0.0288);Gain of phosphorylation at M220 (P = 0.0288);Gain of phosphorylation at M220 (P = 0.0288);.;
MVP		0.88
MPC		1.4
ClinPred		0.89	D
GERP RS		6.1
Varity_R		0.61
gMVP		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

No publications associated with this variant yet.

Other links and lift over

hg19: chr11-27679453;