rs17309874

chr11-27645689-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_033312.1(BDNF-AS):n.305+5684G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 152,214 control chromosomes in the GnomAD database, including 3,168 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 0.19 (3168 hom., cov: 33)
• Consequence: BDNF-AS NR_033312.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.235

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BDNF-AS	NR_033312.1	n.305+5684G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BDNF-AS	ENST00000651238.1	n.379+5684G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28629 AN: 152096 Hom.: 3167 Cov.: 33

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.00965

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.188 AC: 28637 AN: 152214 Hom.: 3168 Cov.: 33 AF XY: 0.184 AC XY: 13692 AN XY: 74426

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.188

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.00967

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.281

Gnomad4 NFE AF: 0.249

Gnomad4 OTH AF: 0.198

Alfa AF: 0.210 Hom.: 460

Bravo AF: 0.181

Asia WGS AF: 0.0910 AC: 316 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	2.0
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17309874; hg19: chr11-27667236;