11-27654165-C-T

Variant names:

• chr11-27654165-C-T
• rs1519480
• ENST00000499008.8:n.375-4076C>T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000499008.8(BDNF-AS):​n.375-4076C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.548 in 152,070 control chromosomes in the GnomAD database, including 26,011 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 0.55 (26011 hom., cov: 33)
• Consequence: BDNF-AS ENST00000499008.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.818

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BDNF-AS	NR_002832.2	n.375-4076C>T		intron_variant	Intron 4 of 7
BDNF-AS	NR_033312.1	n.306-4076C>T		intron_variant	Intron 3 of 8
BDNF-AS	NR_033313.1	n.306-4076C>T		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BDNF-AS	ENST00000499008.8	n.375-4076C>T		intron_variant	Intron 4 of 7	1
BDNF-AS	ENST00000499568.3	n.306-4076C>T		intron_variant	Intron 3 of 8	1
BDNF-AS	ENST00000500662.7	n.306-4076C>T		intron_variant	Intron 3 of 6	1

Frequencies

GnomAD3 genomes AF: 0.548 AC: 83345 AN: 151952 Hom.: 26014 Cov.: 33

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.780

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.816

Gnomad EAS AF: 0.751

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.651

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.548 AC: 83337 AN: 152070 Hom.: 26011 Cov.: 33 AF XY: 0.550 AC XY: 40865 AN XY: 74342

Gnomad4 AFR AF: 0.238

Gnomad4 AMR AF: 0.513

Gnomad4 ASJ AF: 0.816

Gnomad4 EAS AF: 0.752

Gnomad4 SAS AF: 0.625

Gnomad4 FIN AF: 0.651

Gnomad4 NFE AF: 0.689

Gnomad4 OTH AF: 0.588

Alfa AF: 0.674 Hom.: 58756

Bravo AF: 0.523

Asia WGS AF: 0.614 AC: 2135 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	18
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1519480; hg19: chr11-27675712;