rs2203877

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.475 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BDNF-AS	NR_002832.2	n.375-8878T>C		intron_variant	Intron 4 of 7
BDNF-AS	NR_033312.1	n.306-8878T>C		intron_variant	Intron 3 of 8
BDNF-AS	NR_033313.1	n.306-8878T>C		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BDNF-AS	ENST00000499008.8	n.375-8878T>C		intron_variant	Intron 4 of 7	1
BDNF-AS	ENST00000499568.3	n.306-8878T>C		intron_variant	Intron 3 of 8	1
BDNF-AS	ENST00000500662.7	n.306-8878T>C		intron_variant	Intron 3 of 6	1

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

Gnomad4 AFR AF: 0.172

Gnomad4 AMR AF: 0.328

Gnomad4 ASJ AF: 0.512

Gnomad4 EAS AF: 0.278

Gnomad4 SAS AF: 0.317

Gnomad4 FIN AF: 0.491

Gnomad4 NFE AF: 0.479

Gnomad4 OTH AF: 0.396

Alfa AF: 0.427 Hom.: 6479

Bravo AF: 0.346

Asia WGS AF: 0.298 AC: 1038 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2203877; hg19: chr11-27670910;