11-27650705-C-G

Variant names:

• chr11-27650705-C-G
• rs10767658
• ENST00000499008.8:n.375-7536C>G

Variant summary

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

The ENST00000499008.8(BDNF-AS):​n.375-7536C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.725 in 152,038 control chromosomes in the GnomAD database, including 40,186 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 0.72 (40186 hom., cov: 32)
• Consequence: BDNF-AS ENST00000499008.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.398
• Publications: 14 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.926 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000499008.8. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BDNF-AS	NR_002832.2		n.375-7536C>G		intron	N/A
	BDNF-AS	NR_033312.1		n.306-7536C>G		intron	N/A
	BDNF-AS	NR_033313.1		n.306-7536C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BDNF-AS	ENST00000499008.8	TSL:1	n.375-7536C>G		intron	N/A
	BDNF-AS	ENST00000499568.3	TSL:1	n.306-7536C>G		intron	N/A
	BDNF-AS	ENST00000500662.7	TSL:1	n.306-7536C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.725 AC: 110156 AN: 151920 Hom.: 40164 Cov.: 32

Gnomad AFR AF: 0.739

Gnomad AMI AF: 0.797

Gnomad AMR AF: 0.761

Gnomad ASJ AF: 0.830

Gnomad EAS AF: 0.949

Gnomad SAS AF: 0.653

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.700

Gnomad OTH AF: 0.730

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

GnomAD4 genome AF: 0.725 AC: 110225 AN: 152038 Hom.: 40186 Cov.: 32 AF XY: 0.726 AC XY: 53977 AN XY: 74320

African (AFR) AF: 0.739 AC: 30635 AN: 41476

American (AMR) AF: 0.761 AC: 11643 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.830 AC: 2883 AN: 3472

East Asian (EAS) AF: 0.948 AC: 4889 AN: 5156

South Asian (SAS) AF: 0.652 AC: 3134 AN: 4808

European-Finnish (FIN) AF: 0.657 AC: 6932 AN: 10552

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.701 AC: 47615 AN: 67972

Other (OTH) AF: 0.728 AC: 1535 AN: 2108

Alfa AF: 0.622 Hom.: 1728

Bravo AF: 0.735

Asia WGS AF: 0.739 AC: 2570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.84
DANN	Benign	0.31
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs10767658; hg19: chr11-27672252;