rs7934165

Positions:

• chr11-27710436-G-A

Variant summary

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

The ENST00000530663.1(ENSG00000255496):​n.148-13914C>T 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 0.485 in 151,988 control chromosomes in the GnomAD database, including 18,106 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 0.49 (18106 hom., cov: 32)
• Consequence: ENST00000530663.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.82

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=-0.47).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.541 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BDNF	NM_001143805.1	c.-22+10208C>T		intron_variant			NP_001137277.1
BDNF	NM_001143806.1	c.-22+9993C>T		intron_variant			NP_001137278.1
BDNF	NM_001143807.2	c.-22+9075C>T		intron_variant			NP_001137279.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000530663.1	n.148-13914C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73687 AN: 151870 Hom.: 18102 Cov.: 32

Gnomad AFR AF: 0.479

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.485 AC: 73716 AN: 151988 Hom.: 18106 Cov.: 32 AF XY: 0.485 AC XY: 36067 AN XY: 74296

Gnomad4 AFR AF: 0.478

Gnomad4 AMR AF: 0.551

Gnomad4 ASJ AF: 0.512

Gnomad4 EAS AF: 0.446

Gnomad4 SAS AF: 0.333

Gnomad4 FIN AF: 0.491

Gnomad4 NFE AF: 0.486

Gnomad4 OTH AF: 0.487

Alfa AF: 0.485 Hom.: 37174

Bravo AF: 0.489

Asia WGS AF: 0.378 AC: 1315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	16
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7934165; hg19: chr11-27731983;