rs11030064

chr11-27596469-C-T

Variant summary

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

The NR_033312.1(BDNF-AS):n.145-43376C>T 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 0.411 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 NR_033312.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.496

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=-0.88).
• 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/exons	MANE	UniProt
BDNF-AS	NR_033312.1	n.145-43376C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BDNF-AS	ENST00000651238.1	n.218+12132C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.165

Gnomad4 AMR AF: 0.340

Gnomad4 ASJ AF: 0.542

Gnomad4 EAS AF: 0.436

Gnomad4 SAS AF: 0.541

Gnomad4 FIN AF: 0.564

Gnomad4 NFE AF: 0.535

Gnomad4 OTH AF: 0.422

Alfa AF: 0.458 Hom.: 3055

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11030064; hg19: chr11-27618016;