rs2203877

Variant names:

• chr11-27649363-T-C
• rs2203877
• ENST00000499008.8:n.375-8878T>C

Variant summary

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

The ENST00000499008.8(BDNF-AS):​n.375-8878T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.368 in 152,030 control chromosomes in the GnomAD database, including 11,871 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 0.37 (11871 hom., cov: 32)
• Consequence: BDNF-AS ENST00000499008.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.251
• Publications: 16 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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.475 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.375-8878T>C		intron	N/A
	BDNF-AS	NR_033312.1		n.306-8878T>C		intron	N/A
	BDNF-AS	NR_033313.1		n.306-8878T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BDNF-AS	ENST00000499008.8	TSL:1	n.375-8878T>C		intron	N/A
	BDNF-AS	ENST00000499568.3	TSL:1	n.306-8878T>C		intron	N/A
	BDNF-AS	ENST00000500662.7	TSL:1	n.306-8878T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.369 AC: 56000 AN: 151910 Hom.: 11874 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.368 AC: 56000 AN: 152030 Hom.: 11871 Cov.: 32 AF XY: 0.368 AC XY: 27355 AN XY: 74324

African (AFR) AF: 0.172 AC: 7113 AN: 41466

American (AMR) AF: 0.328 AC: 5004 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.512 AC: 1775 AN: 3470

East Asian (EAS) AF: 0.278 AC: 1434 AN: 5164

South Asian (SAS) AF: 0.317 AC: 1532 AN: 4826

European-Finnish (FIN) AF: 0.491 AC: 5176 AN: 10552

Middle Eastern (MID) AF: 0.514 AC: 150 AN: 292

European-Non Finnish (NFE) AF: 0.479 AC: 32576 AN: 67968

Other (OTH) AF: 0.396 AC: 837 AN: 2112

Alfa AF: 0.427 Hom.: 7313

Bravo AF: 0.346

Asia WGS AF: 0.298 AC: 1038 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.7
DANN	Benign	0.62
PhyloP100		-0.25

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: rs2203877;

hg19: chr11-27670910;