rs11030119

chr11-27706555-G-Achr11-27706555-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000314915.6(BDNF):c.3+14857C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 152,080 control chromosomes in the GnomAD database, including 6,137 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 0.28 (6137 hom., cov: 33)
• Consequence: BDNF ENST00000314915.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.221

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BDNF	NM_001143805.1	c.-22+14089C>T		intron_variant
BDNF	NM_001143806.1	c.-22+13874C>T		intron_variant
BDNF	NM_001143807.2	c.-22+12956C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000530663.1	n.148-10033C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42409 AN: 151962 Hom.: 6121 Cov.: 33

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.0523

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.279 AC: 42466 AN: 152080 Hom.: 6137 Cov.: 33 AF XY: 0.279 AC XY: 20709 AN XY: 74350

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.181

Gnomad4 EAS AF: 0.0527

Gnomad4 SAS AF: 0.350

Gnomad4 FIN AF: 0.341

Gnomad4 NFE AF: 0.292

Gnomad4 OTH AF: 0.273

Alfa AF: 0.262 Hom.: 5626

Bravo AF: 0.271

Asia WGS AF: 0.263 AC: 916 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
Cadd	Benign	13
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11030119; hg19: chr11-27728102;