Variant chr11-27617387-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000499008.8(BDNF-AS):n.214-22458C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.736 in 152,018 control chromosomes in the GnomAD database, including 41,811 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 ( 41811 hom., cov: 31)

Consequence

BDNF-AS
ENST00000499008.8 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.420

Variant links:

Genes affected

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

BDNF-AS links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.79 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
BDNF-AS	NR_002832.2 link	n.214-22458C>A	intron_variant
BDNF-AS	NR_033312.1 link	n.145-22458C>A	intron_variant
BDNF-AS	NR_033313.1 link	n.145-22458C>A	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
BDNF-AS	ENST00000499008.8 link	n.214-22458C>A	intron_variant	1
BDNF-AS	ENST00000499568.3 link	n.145-22458C>A	intron_variant	1
BDNF-AS	ENST00000500662.7 link	n.145-22458C>A	intron_variant	1

Frequencies

GnomAD3 genomes

AF:

0.736

AC:

111730

AN:

151898

Hom.:

41769

Cov.:

show subpopulations

Gnomad AFR

AF:

0.620

Gnomad AMI

AF:

0.664

Gnomad AMR

AF:

0.786

Gnomad ASJ

AF:

0.729

Gnomad EAS

AF:

0.518

Gnomad SAS

AF:

0.737

Gnomad FIN

AF:

0.840

Gnomad MID

AF:

0.777

Gnomad NFE

AF:

0.795

Gnomad OTH

AF:

0.745

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

GnomAD4 genome

AF:

0.736

AC:

111827

AN:

152018

Hom.:

41811

Cov.:

AF XY:

0.737

AC XY:

54791

AN XY:

74326

show subpopulations

Gnomad4 AFR

AF:

0.621

Gnomad4 AMR

AF:

0.786

Gnomad4 ASJ

AF:

0.729

Gnomad4 EAS

AF:

0.518

Gnomad4 SAS

AF:

0.738

Gnomad4 FIN

AF:

0.840

Gnomad4 NFE

AF:

0.795

Gnomad4 OTH

AF:

0.745

Alfa

AF:

0.762

Hom.:

6951

Bravo

AF:

0.725

Asia WGS

AF:

0.684

AC:

2381

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.46

DANN

Benign

0.59

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over