chr11-27635242-G-T

Variant summary

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

The ENST00000499008.8(BDNF-AS):​n.214-4603G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 152,158 control chromosomes in the GnomAD database, including 3,405 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 0.20 ( 3405 hom., cov: 32)

Consequence

BDNF-AS
ENST00000499008.8 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.44

Publications

19 publications found
Variant links:
Genes affected
BDNF-AS (HGNC:20608): (BDNF antisense RNA)

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=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
BDNF-ASNR_002832.2 linkn.214-4603G>T intron_variant Intron 3 of 7
BDNF-ASNR_033312.1 linkn.145-4603G>T intron_variant Intron 2 of 8
BDNF-ASNR_033313.1 linkn.145-4603G>T intron_variant Intron 2 of 5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
BDNF-ASENST00000499008.8 linkn.214-4603G>T intron_variant Intron 3 of 7 1
BDNF-ASENST00000499568.3 linkn.145-4603G>T intron_variant Intron 2 of 8 1
BDNF-ASENST00000500662.7 linkn.145-4603G>T intron_variant Intron 2 of 6 1

Frequencies

GnomAD3 genomes
AF:
0.203
AC:
30814
AN:
152040
Hom.:
3401
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.169
Gnomad AMI
AF:
0.336
Gnomad AMR
AF:
0.192
Gnomad ASJ
AF:
0.271
Gnomad EAS
AF:
0.443
Gnomad SAS
AF:
0.267
Gnomad FIN
AF:
0.160
Gnomad MID
AF:
0.212
Gnomad NFE
AF:
0.204
Gnomad OTH
AF:
0.206
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.203
AC:
30835
AN:
152158
Hom.:
3405
Cov.:
32
AF XY:
0.203
AC XY:
15138
AN XY:
74398
show subpopulations
African (AFR)
AF:
0.170
AC:
7038
AN:
41500
American (AMR)
AF:
0.192
AC:
2937
AN:
15296
Ashkenazi Jewish (ASJ)
AF:
0.271
AC:
939
AN:
3470
East Asian (EAS)
AF:
0.443
AC:
2293
AN:
5178
South Asian (SAS)
AF:
0.267
AC:
1286
AN:
4820
European-Finnish (FIN)
AF:
0.160
AC:
1698
AN:
10582
Middle Eastern (MID)
AF:
0.221
AC:
65
AN:
294
European-Non Finnish (NFE)
AF:
0.204
AC:
13839
AN:
67996
Other (OTH)
AF:
0.206
AC:
434
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1235
2470
3705
4940
6175
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
330
660
990
1320
1650
<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:
0.209
Hom.:
4568
Bravo
AF:
0.206
Asia WGS
AF:
0.294
AC:
1022
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
0.16
DANN
Benign
0.45
PhyloP100
-1.4

Splicing

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

Publications

Other links and lift over

dbSNP: rs4923460; hg19: chr11-27656789; API