rs4923460

chr11-27635242-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_033312.1(BDNF-AS):n.145-4603G>T variant causes a intron, non coding transcript 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 NR_033312.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44

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=-0.89).
• 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/exons	MANE	UniProt
BDNF-AS	NR_033312.1	n.145-4603G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BDNF-AS	ENST00000651238.1	n.219-4603G>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.170

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.271

Gnomad4 EAS AF: 0.443

Gnomad4 SAS AF: 0.267

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.204

Gnomad4 OTH AF: 0.206

Alfa AF: 0.198 Hom.: 499

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4923460; hg19: chr11-27656789;