Genetic Variant BDNF:n.118C>T (chr11-27701516-G-A) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The ENST00000584049.5(BDNF):n.118C>T variant causes a non coding transcript exon change. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

BDNF
ENST00000584049.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.61

Publications

5 publications found

Variant links:

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]

BDNF links:

ENSG00000255496 (HGNC:):

ENSG00000255496 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.34).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000584049.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank	Protein
BDNF	NM_170733.4	c.-241C>T	5_prime_UTR	Exon 1 of 2	NP_733929.1
BDNF	NM_170731.5	c.3+19896C>T	intron	N/A	NP_733927.1
BDNF	NM_001143805.1	c.-22+19128C>T	intron	N/A	NP_001137277.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
BDNF	ENST00000584049.5	TSL:1	n.118C>T	non_coding_transcript_exon	Exon 1 of 2
BDNF	ENST00000314915.6	TSL:1	c.3+19896C>T	intron	N/A	ENSP00000320002.6
BDNF	ENST00000395978.7	TSL:1	c.-22+18913C>T	intron	N/A	ENSP00000379302.3

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

836158

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

386316

African (AFR)

AF:

0.00

AC:

AN:

15828

American (AMR)

AF:

0.00

AC:

AN:

1460

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

5200

East Asian (EAS)

AF:

0.00

AC:

AN:

3794

South Asian (SAS)

AF:

0.00

AC:

AN:

16710

European-Finnish (FIN)

AF:

0.00

AC:

AN:

370

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1630

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

763768

Other (OTH)

AF:

0.00

AC:

AN:

27398

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.34

CADD

Benign

(source)

DANN

Benign

0.93

PhyloP100

4.6

PromoterAI

0.19

Neutral

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over