Genetic Variant BDNF:n.*2655C>A (chr11-27656039-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000530786.5(BDNF):n.*2655C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,006 control chromosomes in the GnomAD database, including 2,876 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 0.17 ( 2876 hom., cov: 31)

Exomes 𝑓: 0.10 ( 0 hom. )

Consequence

BDNF
ENST00000530786.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.43

Publications

32 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:

BDNF-AS (HGNC:20608): (BDNF antisense RNA)

BDNF-AS links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000530786.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
BDNF	NM_001709.5	MANE Select	c.*1782C>A	3_prime_UTR	Exon 2 of 2	NP_001700.2
BDNF	NM_001143810.2		c.*1782C>A	3_prime_UTR	Exon 3 of 3	NP_001137282.1
BDNF	NM_001143809.2		c.*1782C>A	3_prime_UTR	Exon 2 of 2	NP_001137281.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
BDNF	ENST00000530786.5	TSL:1	n.*2655C>A	non_coding_transcript_exon	Exon 4 of 4	ENSP00000433003.1
BDNF	ENST00000584049.5	TSL:1	n.2884C>A	non_coding_transcript_exon	Exon 2 of 2
BDNF	ENST00000356660.9	TSL:1 MANE Select	c.*1782C>A	3_prime_UTR	Exon 2 of 2	ENSP00000349084.4

Frequencies

GnomAD3 genomes

AF:

0.172

AC:

26116

AN:

151846

Hom.:

2878

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0626

Gnomad AMI

AF:

0.330

Gnomad AMR

AF:

0.179

Gnomad ASJ

AF:

0.270

Gnomad EAS

AF:

0.465

Gnomad SAS

AF:

0.263

Gnomad FIN

AF:

0.160

Gnomad MID

AF:

0.206

Gnomad NFE

AF:

0.203

Gnomad OTH

AF:

0.189

GnomAD4 exome

AF:

0.100

AC:

AN:

Hom.:

Cov.:

AF XY:

0.0769

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.250

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0357

AC:

AN:

Other (OTH)

AF:

0.167

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.450

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.172

AC:

26110

AN:

151966

Hom.:

2876

Cov.:

AF XY:

0.173

AC XY:

12880

AN XY:

74280

show subpopulations

African (AFR)

AF:

0.0624

AC:

2589

AN:

41518

American (AMR)

AF:

0.179

AC:

2729

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.270

AC:

936

AN:

3464

East Asian (EAS)

AF:

0.464

AC:

2366

AN:

5096

South Asian (SAS)

AF:

0.263

AC:

1264

AN:

4814

European-Finnish (FIN)

AF:

0.160

AC:

1692

AN:

10570

Middle Eastern (MID)

AF:

0.214

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.203

AC:

13776

AN:

67934

Other (OTH)

AF:

0.188

AC:

397

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1052

2104

3156

4208

5260

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

290

580

870

1160

1450

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.174

Hom.:

578

Bravo

AF:

0.171

Asia WGS

AF:

0.294

AC:

1022

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

6.7

(source)

DANN

Benign

0.71

PhyloP100

1.4

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over