11-27635363-A-G

Variant names:

• chr11-27635363-A-G
• rs4923461
• ENST00000499008.8:n.214-4482A>G

Variant summary

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

The ENST00000499008.8(BDNF-AS):​n.214-4482A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 152,182 control chromosomes in the GnomAD database, including 3,405 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 0.20 (3405 hom., cov: 32)
• Consequence: BDNF-AS ENST00000499008.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0740

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 (EAS) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BDNF-AS	NR_002832.2	n.214-4482A>G		intron_variant	Intron 3 of 7
BDNF-AS	NR_033312.1	n.145-4482A>G		intron_variant	Intron 2 of 8
BDNF-AS	NR_033313.1	n.145-4482A>G		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BDNF-AS	ENST00000499008.8	n.214-4482A>G		intron_variant	Intron 3 of 7	1
BDNF-AS	ENST00000499568.3	n.145-4482A>G		intron_variant	Intron 2 of 8	1
BDNF-AS	ENST00000500662.7	n.145-4482A>G		intron_variant	Intron 2 of 6	1

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30817 AN: 152066 Hom.: 3401 Cov.: 32

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.444

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.203 AC: 30837 AN: 152182 Hom.: 3405 Cov.: 32 AF XY: 0.204 AC XY: 15145 AN XY: 74400

Gnomad4 AFR AF: 0.170

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.270

Gnomad4 EAS AF: 0.444

Gnomad4 SAS AF: 0.267

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.203

Gnomad4 OTH AF: 0.206

Alfa AF: 0.189 Hom.: 1389

Bravo AF: 0.206

Asia WGS AF: 0.294 AC: 1024 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	7.8
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: rs4923461; hg19: chr11-27656910;