rs11030064

Variant names:

• chr11-27596469-C-T
• rs11030064
• ENST00000499008.8:n.213+12132C>T

Variant summary

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

The ENST00000499008.8(BDNF-AS):​n.213+12132C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 152,028 control chromosomes in the GnomAD database, including 15,009 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 0.41 (15009 hom., cov: 32)
• Consequence: BDNF-AS ENST00000499008.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.496
• Publications: 7 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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.53 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BDNF-AS	NR_002832.2	n.213+12132C>T		intron_variant	Intron 3 of 7
BDNF-AS	NR_033312.1	n.145-43376C>T		intron_variant	Intron 2 of 8
BDNF-AS	NR_033313.1	n.145-43376C>T		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BDNF-AS	ENST00000499008.8	n.213+12132C>T		intron_variant	Intron 3 of 7	1
BDNF-AS	ENST00000499568.3	n.145-43376C>T		intron_variant	Intron 2 of 8	1
BDNF-AS	ENST00000500662.7	n.145-43376C>T		intron_variant	Intron 2 of 6	1

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62495 AN: 151910 Hom.: 14999 Cov.: 32

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.436

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.411 AC: 62520 AN: 152028 Hom.: 15009 Cov.: 32 AF XY: 0.416 AC XY: 30890 AN XY: 74294

African (AFR) AF: 0.165 AC: 6830 AN: 41486

American (AMR) AF: 0.340 AC: 5186 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.542 AC: 1882 AN: 3472

East Asian (EAS) AF: 0.436 AC: 2247 AN: 5156

South Asian (SAS) AF: 0.541 AC: 2602 AN: 4810

European-Finnish (FIN) AF: 0.564 AC: 5962 AN: 10566

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.535 AC: 36330 AN: 67964

Other (OTH) AF: 0.422 AC: 886 AN: 2102

Alfa AF: 0.450 Hom.: 3070

Bravo AF: 0.377

Asia WGS AF: 0.499 AC: 1735 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	1.8
DANN	Benign	0.76
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs11030064; hg19: chr11-27618016;