chr11-27704439-T-A

Variant names:

• chr11-27704439-T-A
• rs10767664
• ENST00000314915.6:c.3+16973A>T

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4 BA1

The ENST00000314915.6(BDNF):​c.3+16973A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.822 in 152,122 control chromosomes in the GnomAD database, including 52,059 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.82 (52059 hom., cov: 31)
• Consequence: BDNF ENST00000314915.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.69
• Publications: 173 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: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.16).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.928 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BDNF	NM_170731.5	c.3+16973A>T		intron_variant	Intron 1 of 1		NP_733927.1
BDNF	NM_001143805.1	c.-22+16205A>T		intron_variant	Intron 1 of 1		NP_001137277.1
BDNF	NM_001143806.1	c.-22+15990A>T		intron_variant	Intron 1 of 1		NP_001137278.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BDNF	ENST00000314915.6	c.3+16973A>T		intron_variant	Intron 1 of 1	1		ENSP00000320002.6
BDNF	ENST00000395978.7	c.-22+15990A>T		intron_variant	Intron 1 of 1	1		ENSP00000379302.3
BDNF	ENST00000395981.7	c.-22+15907A>T		intron_variant	Intron 1 of 1	1		ENSP00000379305.3

Frequencies

GnomAD3 genomes AF: 0.821 AC: 124863 AN: 152004 Hom.: 52002 Cov.: 31

Gnomad AFR AF: 0.936

Gnomad AMI AF: 0.665

Gnomad AMR AF: 0.821

Gnomad ASJ AF: 0.707

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.695

Gnomad FIN AF: 0.837

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.789

Gnomad OTH AF: 0.803

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.822 AC: 124982 AN: 152122 Hom.: 52059 Cov.: 31 AF XY: 0.820 AC XY: 60952 AN XY: 74366

African (AFR) AF: 0.936 AC: 38850 AN: 41508

American (AMR) AF: 0.821 AC: 12556 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.707 AC: 2450 AN: 3466

East Asian (EAS) AF: 0.530 AC: 2744 AN: 5176

South Asian (SAS) AF: 0.696 AC: 3348 AN: 4808

European-Finnish (FIN) AF: 0.837 AC: 8856 AN: 10582

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.789 AC: 53651 AN: 67982

Other (OTH) AF: 0.803 AC: 1694 AN: 2110

Alfa AF: 0.817 Hom.: 6343

Bravo AF: 0.825

Asia WGS AF: 0.679 AC: 2359 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.16
CADD	Benign	17
DANN	Benign	0.81
PhyloP100		2.7
Mutation Taster		=94/6	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10767664; hg19: chr11-27725986;