11-27699390-C-G

Variant names:

• chr11-27699390-C-G
• rs66866077
• ENST00000395986.6:c.16G>C

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_170734.4(BDNF):​c.16G>C​(p.Glu6Gln) variant causes a missense 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. 14/17 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E6K) has been classified as Benign.

• Frequency: Genomes: not found (cov: 31)
• Consequence: BDNF NM_170734.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.310
• Publications: 18 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]

ENSG00000255496 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.11542067).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_170734.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BDNF	NM_001709.5	MANE Select	c.-22+774G>C		intron	N/A	NP_001700.2
	BDNF	NM_170734.4		c.16G>C	p.Glu6Gln	missense	Exon 1 of 2	NP_733930.1
	BDNF	NM_001143810.2		c.-59+1581G>C		intron	N/A	NP_001137282.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BDNF	ENST00000395986.6	TSL:1	c.16G>C	p.Glu6Gln	missense	Exon 1 of 2	ENSP00000379309.2
	BDNF	ENST00000356660.9	TSL:1 MANE Select	c.-22+774G>C		intron	N/A	ENSP00000349084.4
	BDNF	ENST00000438929.5	TSL:1	c.-59+1581G>C		intron	N/A	ENSP00000414303.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.12
BayesDel_addAF	Benign	-0.18	T
BayesDel_noAF	Benign	-0.50
CADD	Benign	8.4
DANN	Benign	0.75
Eigen	Benign	-0.49
Eigen_PC	Benign	-0.68
FATHMM_MKL	Benign	0.048	N
LIST_S2	Benign	0.34	T
M_CAP	Benign	0.047	D
MetaRNN	Benign	0.12	T
MetaSVM	Benign	-1.0	T
PhyloP100		0.31
PROVEAN	Benign	0.10	N
REVEL	Benign	0.053
Sift	Pathogenic	0.0	D
Sift4G	Benign	0.76	T
Polyphen		0.94	P
Vest4		0.094
MutPred		0.16		Gain of MoRF binding (P = 0.0189)
MVP		0.48
ClinPred		0.94	D
GERP RS		0.20
PromoterAI		0.017	Neutral
Mutation Taster		=100/0	polymorphism

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs66866077; hg19: chr11-27720937;