Genetic Variant ENST00000499008.8:n.375-7288A>G (chr11-27650953-A-G) – 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.375-7288A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 152,256 control chromosomes in the GnomAD database, including 2,966 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 ( 2966 hom., cov: 33)

Consequence

BDNF-AS
ENST00000499008.8 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.65

Publications

20 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=-0.75).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
BDNF-AS	NR_002832.2 link	n.375-7288A>G	intron_variant	Intron 4 of 7
BDNF-AS	NR_033312.1 link	n.306-7288A>G	intron_variant	Intron 3 of 8
BDNF-AS	NR_033313.1 link	n.306-7288A>G	intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
BDNF-AS	ENST00000499008.8 link	n.375-7288A>G	intron_variant	Intron 4 of 7	1
BDNF-AS	ENST00000499568.3 link	n.306-7288A>G	intron_variant	Intron 3 of 8	1
BDNF-AS	ENST00000500662.7 link	n.306-7288A>G	intron_variant	Intron 3 of 6	1

Frequencies

GnomAD3 genomes

AF:

0.174

AC:

26401

AN:

152140

Hom.:

2968

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0647

Gnomad AMI

AF:

0.336

Gnomad AMR

AF:

0.180

Gnomad ASJ

AF:

0.271

Gnomad EAS

AF:

0.473

Gnomad SAS

AF:

0.264

Gnomad FIN

AF:

0.160

Gnomad MID

AF:

0.206

Gnomad NFE

AF:

0.204

Gnomad OTH

AF:

0.190

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

GnomAD4 genome

AF:

0.173

AC:

26396

AN:

152256

Hom.:

2966

Cov.:

AF XY:

0.175

AC XY:

13031

AN XY:

74428

show subpopulations

African (AFR)

AF:

0.0645

AC:

2681

AN:

41576

American (AMR)

AF:

0.180

AC:

2750

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.271

AC:

942

AN:

3470

East Asian (EAS)

AF:

0.473

AC:

2439

AN:

5156

South Asian (SAS)

AF:

0.264

AC:

1272

AN:

4826

European-Finnish (FIN)

AF:

0.160

AC:

1696

AN:

10610

Middle Eastern (MID)

AF:

0.214

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.204

AC:

13846

AN:

68010

Other (OTH)

AF:

0.190

AC:

401

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1071

2143

3214

4286

5357

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

294

588

882

1176

1470

<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:

0.200

Hom.:

1068

Bravo

AF:

0.172

Asia WGS

AF:

0.298

AC:

1036

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

(source)

DANN

Benign

0.88

PhyloP100

1.6

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