rs11030121

Positions:

• chr11-27714660-C-T

Variant summary

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

The ENST00000530663.1(ENSG00000255496):​n.148-18138G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 151,720 control chromosomes in the GnomAD database, including 9,263 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 0.34 (9263 hom., cov: 32)
• Consequence: ENST00000530663.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.220

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BDNF	NM_001143805.1	c.-22+5984G>A		intron_variant			NP_001137277.1
BDNF	NM_001143806.1	c.-22+5769G>A		intron_variant			NP_001137278.1
BDNF	NM_001143807.2	c.-22+4851G>A		intron_variant			NP_001137279.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000530663.1	n.148-18138G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51079 AN: 151602 Hom.: 9224 Cov.: 32

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.0841

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.337 AC: 51169 AN: 151720 Hom.: 9263 Cov.: 32 AF XY: 0.335 AC XY: 24815 AN XY: 74100

Gnomad4 AFR AF: 0.459

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.0837

Gnomad4 SAS AF: 0.363

Gnomad4 FIN AF: 0.349

Gnomad4 NFE AF: 0.304

Gnomad4 OTH AF: 0.316

Alfa AF: 0.324 Hom.: 1226

Bravo AF: 0.335

Asia WGS AF: 0.301 AC: 1046 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11030121; hg19: chr11-27736207;