Genetic Variant BDNF-AS:n.48-13741G>A (chr11-27526279-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000499008.8(BDNF-AS):n.48-13741G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.745 in 152,016 control chromosomes in the GnomAD database, including 42,545 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 0.74 ( 42545 hom., cov: 31)

Consequence

BDNF-AS
ENST00000499008.8 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.546

Publications

2 publications found

Variant links:

Genes affected

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

BDNF-AS links:

Genome browser will be placed here

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=-0.94).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.854 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
BDNF-AS	NR_002832.2 link	n.48-13741G>A	intron_variant	Intron 1 of 7
BDNF-AS	NR_033312.1 link	n.48-13741G>A	intron_variant	Intron 1 of 8
BDNF-AS	NR_033313.1 link	n.48-13741G>A	intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
BDNF-AS	ENST00000499008.8 link	n.48-13741G>A	intron_variant	Intron 1 of 7	1
BDNF-AS	ENST00000499568.3 link	n.48-13741G>A	intron_variant	Intron 1 of 8	1
BDNF-AS	ENST00000500662.7 link	n.48-13741G>A	intron_variant	Intron 1 of 6	1

Frequencies

GnomAD3 genomes

AF:

0.745

AC:

113153

AN:

151898

Hom.:

42516

Cov.:

show subpopulations

Gnomad AFR

AF:

0.678

Gnomad AMI

AF:

0.822

Gnomad AMR

AF:

0.659

Gnomad ASJ

AF:

0.856

Gnomad EAS

AF:

0.749

Gnomad SAS

AF:

0.875

Gnomad FIN

AF:

0.791

Gnomad MID

AF:

0.815

Gnomad NFE

AF:

0.781

Gnomad OTH

AF:

0.747

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

GnomAD4 genome

AF:

0.745

AC:

113224

AN:

152016

Hom.:

42545

Cov.:

AF XY:

0.749

AC XY:

55628

AN XY:

74300

show subpopulations

African (AFR)

AF:

0.678

AC:

28115

AN:

41462

American (AMR)

AF:

0.658

AC:

10056

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.856

AC:

2971

AN:

3472

East Asian (EAS)

AF:

0.749

AC:

3841

AN:

5128

South Asian (SAS)

AF:

0.876

AC:

4222

AN:

4820

European-Finnish (FIN)

AF:

0.791

AC:

8365

AN:

10572

Middle Eastern (MID)

AF:

0.836

AC:

244

AN:

292

European-Non Finnish (NFE)

AF:

0.781

AC:

53093

AN:

67978

Other (OTH)

AF:

0.747

AC:

1571

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1425

2851

4276

5702

7127

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

856

1712

2568

3424

4280

<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:

0.760

Hom.:

5713

Bravo

AF:

0.724

Asia WGS

AF:

0.798

AC:

2775

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.76

(source)

DANN

Benign

0.52

PhyloP100

-0.55

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over