chr11-27650953-A-G

Variant names:

• chr11-27650953-A-G
• rs4923463
• ENST00000499008.8:n.375-7288A>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.375-7288A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 152,256 control chromosomes in the GnomAD database, including 2,966 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 0.17 (2966 hom., cov: 33)
• Consequence: BDNF-AS ENST00000499008.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.65
• Publications: 20 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=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.457 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.375-7288A>G		intron	N/A
	BDNF-AS	NR_033312.1		n.306-7288A>G		intron	N/A
	BDNF-AS	NR_033313.1		n.306-7288A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BDNF-AS	ENST00000499008.8	TSL:1	n.375-7288A>G		intron	N/A
	BDNF-AS	ENST00000499568.3	TSL:1	n.306-7288A>G		intron	N/A
	BDNF-AS	ENST00000500662.7	TSL:1	n.306-7288A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26401 AN: 152140 Hom.: 2968 Cov.: 33

Gnomad AFR AF: 0.0647

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.173 AC: 26396 AN: 152256 Hom.: 2966 Cov.: 33 AF XY: 0.175 AC XY: 13031 AN XY: 74428

African (AFR) AF: 0.0645 AC: 2681 AN: 41576

American (AMR) AF: 0.180 AC: 2750 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 942 AN: 3470

East Asian (EAS) AF: 0.473 AC: 2439 AN: 5156

South Asian (SAS) AF: 0.264 AC: 1272 AN: 4826

European-Finnish (FIN) AF: 0.160 AC: 1696 AN: 10610

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.204 AC: 13846 AN: 68010

Other (OTH) AF: 0.190 AC: 401 AN: 2112

Alfa AF: 0.200 Hom.: 1068

Bravo AF: 0.172

Asia WGS AF: 0.298 AC: 1036 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	15
DANN	Benign	0.88
PhyloP100		1.6

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4923463;

hg19: chr11-27672500;