chr11-27635242-G-T

Variant names:

• chr11-27635242-G-T
• rs4923460
• ENST00000499008.8:n.214-4603G>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.214-4603G>T 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 152,158 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: -1.44
• Publications: 19 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=-0.89).
• 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.214-4603G>T		intron_variant	Intron 3 of 7
BDNF-AS	NR_033312.1	n.145-4603G>T		intron_variant	Intron 2 of 8
BDNF-AS	NR_033313.1	n.145-4603G>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.214-4603G>T		intron_variant	Intron 3 of 7	1
BDNF-AS	ENST00000499568.3	n.145-4603G>T		intron_variant	Intron 2 of 8	1
BDNF-AS	ENST00000500662.7	n.145-4603G>T		intron_variant	Intron 2 of 6	1

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30814 AN: 152040 Hom.: 3401 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.203 AC: 30835 AN: 152158 Hom.: 3405 Cov.: 32 AF XY: 0.203 AC XY: 15138 AN XY: 74398

African (AFR) AF: 0.170 AC: 7038 AN: 41500

American (AMR) AF: 0.192 AC: 2937 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 939 AN: 3470

East Asian (EAS) AF: 0.443 AC: 2293 AN: 5178

South Asian (SAS) AF: 0.267 AC: 1286 AN: 4820

European-Finnish (FIN) AF: 0.160 AC: 1698 AN: 10582

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.204 AC: 13839 AN: 67996

Other (OTH) AF: 0.206 AC: 434 AN: 2110

Alfa AF: 0.209 Hom.: 4568

Bravo AF: 0.206

Asia WGS AF: 0.294 AC: 1022 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.16
DANN	Benign	0.45
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs4923460; hg19: chr11-27656789;