rs2030323

chr11-27706992-A-Cchr11-27706992-A-T

Variant summary

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

The ENST00000314915.6(BDNF):c.3+14420T>G 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 152,184 control chromosomes in the GnomAD database, including 52,083 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 (52083 hom., cov: 33)
• Consequence: BDNF ENST00000314915.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178

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=-0.8).
• 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/exons	MANE	UniProt
BDNF	NM_001143805.1	c.-22+13652T>G		intron_variant
BDNF	NM_001143806.1	c.-22+13437T>G		intron_variant
BDNF	NM_001143807.2	c.-22+12519T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000530663.1	n.148-10470T>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.821 AC: 124915 AN: 152066 Hom.: 52026 Cov.: 33

Gnomad AFR AF: 0.936

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.821

Gnomad ASJ AF: 0.707

Gnomad EAS AF: 0.529

Gnomad SAS AF: 0.695

Gnomad FIN AF: 0.837

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.789

Gnomad OTH AF: 0.804

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

GnomAD4 genome AF: 0.822 AC: 125034 AN: 152184 Hom.: 52083 Cov.: 33 AF XY: 0.820 AC XY: 60967 AN XY: 74392

Gnomad4 AFR AF: 0.936

Gnomad4 AMR AF: 0.821

Gnomad4 ASJ AF: 0.707

Gnomad4 EAS AF: 0.529

Gnomad4 SAS AF: 0.696

Gnomad4 FIN AF: 0.837

Gnomad4 NFE AF: 0.789

Gnomad4 OTH AF: 0.804

Alfa AF: 0.782 Hom.: 46168

Bravo AF: 0.825

Asia WGS AF: 0.678 AC: 2358 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	3.8
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2030323; hg19: chr11-27728539;