Genetic Variant ENST00000499008.8:n.48-9185C>T (chr11-27530835-C-T) – 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.48-9185C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,066 control chromosomes in the GnomAD database, including 3,041 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 0.18 ( 3041 hom., cov: 32)

Consequence

BDNF-AS
ENST00000499008.8 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.221

Publications

4 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=-0.85).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
BDNF-AS	NR_002832.2 link	n.48-9185C>T	intron_variant	Intron 1 of 7
BDNF-AS	NR_033312.1 link	n.48-9185C>T	intron_variant	Intron 1 of 8
BDNF-AS	NR_033313.1 link	n.48-9185C>T	intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
BDNF-AS	ENST00000499008.8 link	n.48-9185C>T	intron_variant	Intron 1 of 7	1
BDNF-AS	ENST00000499568.3 link	n.48-9185C>T	intron_variant	Intron 1 of 8	1
BDNF-AS	ENST00000500662.7 link	n.48-9185C>T	intron_variant	Intron 1 of 6	1

Frequencies

GnomAD3 genomes

AF:

0.176

AC:

26813

AN:

151948

Hom.:

3043

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0455

Gnomad AMI

AF:

0.343

Gnomad AMR

AF:

0.251

Gnomad ASJ

AF:

0.270

Gnomad EAS

AF:

0.0745

Gnomad SAS

AF:

0.253

Gnomad FIN

AF:

0.188

Gnomad MID

AF:

0.231

Gnomad NFE

AF:

0.232

Gnomad OTH

AF:

0.193

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

GnomAD4 genome

AF:

0.176

AC:

26807

AN:

152066

Hom.:

3041

Cov.:

AF XY:

0.176

AC XY:

13096

AN XY:

74322

show subpopulations

African (AFR)

AF:

0.0454

AC:

1884

AN:

41510

American (AMR)

AF:

0.251

AC:

3826

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.270

AC:

938

AN:

3472

East Asian (EAS)

AF:

0.0744

AC:

385

AN:

5172

South Asian (SAS)

AF:

0.253

AC:

1220

AN:

4818

European-Finnish (FIN)

AF:

0.188

AC:

1986

AN:

10548

Middle Eastern (MID)

AF:

0.241

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.232

AC:

15778

AN:

67964

Other (OTH)

AF:

0.193

AC:

407

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1080

2159

3239

4318

5398

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

288

576

864

1152

1440

<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:

0.135

Hom.:

441

Bravo

AF:

0.174

Asia WGS

AF:

0.145

AC:

503

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

6.3

(source)

DANN

Benign

0.62

PhyloP100

0.22

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