rs17309874

Variant names:

• chr11-27645689-G-A
• rs17309874
• ENST00000499008.8:n.374+5684G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000499008.8(BDNF-AS):​n.374+5684G>A variant causes a intron 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 ENST00000499008.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.235
• Publications: 16 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
BDNF-AS	NR_002832.2	n.374+5684G>A		intron_variant	Intron 4 of 7
BDNF-AS	NR_033312.1	n.305+5684G>A		intron_variant	Intron 3 of 8
BDNF-AS	NR_033313.1	n.305+5684G>A		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BDNF-AS	ENST00000499008.8	n.374+5684G>A		intron_variant	Intron 4 of 7	1
BDNF-AS	ENST00000499568.3	n.305+5684G>A		intron_variant	Intron 3 of 8	1
BDNF-AS	ENST00000500662.7	n.305+5684G>A		intron_variant	Intron 3 of 6	1

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

African (AFR) AF: 0.103 AC: 4280 AN: 41534

American (AMR) AF: 0.188 AC: 2872 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 415 AN: 3466

East Asian (EAS) AF: 0.00967 AC: 50 AN: 5172

South Asian (SAS) AF: 0.106 AC: 511 AN: 4822

European-Finnish (FIN) AF: 0.281 AC: 2970 AN: 10588

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.249 AC: 16923 AN: 68016

Other (OTH) AF: 0.198 AC: 419 AN: 2112

Alfa AF: 0.206 Hom.: 463

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
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs17309874; hg19: chr11-27667236;