rs1488830

Variant names:

• chr11-27615338-C-T
• rs1488830
• ENST00000499008.8:n.214-24507C>T

Variant summary

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

The ENST00000499008.8(BDNF-AS):​n.214-24507C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.765 in 152,028 control chromosomes in the GnomAD database, including 44,857 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 0.76 (44857 hom., cov: 31)
• Consequence: BDNF-AS ENST00000499008.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.152
• Publications: 21 publications found

Genes affected

BDNF-AS (HGNC:20608): (BDNF antisense RNA)

LINC00678 (HGNC:44413): (long intergenic non-protein coding RNA 678)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.79 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BDNF-AS	NR_002832.2	n.214-24507C>T		intron_variant	Intron 3 of 7
BDNF-AS	NR_033312.1	n.145-24507C>T		intron_variant	Intron 2 of 8
BDNF-AS	NR_033313.1	n.145-24507C>T		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BDNF-AS	ENST00000499008.8	n.214-24507C>T		intron_variant	Intron 3 of 7	1
BDNF-AS	ENST00000499568.3	n.145-24507C>T		intron_variant	Intron 2 of 8	1
BDNF-AS	ENST00000500662.7	n.145-24507C>T		intron_variant	Intron 2 of 6	1

Frequencies

GnomAD3 genomes AF: 0.765 AC: 116179 AN: 151912 Hom.: 44806 Cov.: 31

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.798

Gnomad ASJ AF: 0.730

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.739

Gnomad FIN AF: 0.840

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.763

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

GnomAD4 genome AF: 0.765 AC: 116284 AN: 152028 Hom.: 44857 Cov.: 31 AF XY: 0.766 AC XY: 56921 AN XY: 74312

African (AFR) AF: 0.723 AC: 29941 AN: 41440

American (AMR) AF: 0.798 AC: 12182 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.730 AC: 2530 AN: 3468

East Asian (EAS) AF: 0.518 AC: 2670 AN: 5158

South Asian (SAS) AF: 0.739 AC: 3551 AN: 4804

European-Finnish (FIN) AF: 0.840 AC: 8885 AN: 10576

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.795 AC: 54081 AN: 67994

Other (OTH) AF: 0.764 AC: 1613 AN: 2112

Alfa AF: 0.779 Hom.: 60269

Bravo AF: 0.759

Asia WGS AF: 0.689 AC: 2399 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.4
DANN	Benign	0.35
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs1488830; hg19: chr11-27636885;