rs2352802

Positions:

• chr11-27526279-G-A

Variant summary

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

The NR_033312.1(BDNF-AS):​n.48-13741G>A 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 0.745 in 152,016 control chromosomes in the GnomAD database, including 42,545 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 0.74 (42545 hom., cov: 31)
• Consequence: BDNF-AS NR_033312.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.546

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=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.854 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BDNF-AS	NR_033312.1	n.48-13741G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BDNF-AS	ENST00000651238.1	n.53-13741G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.745 AC: 113153 AN: 151898 Hom.: 42516 Cov.: 31

Gnomad AFR AF: 0.678

Gnomad AMI AF: 0.822

Gnomad AMR AF: 0.659

Gnomad ASJ AF: 0.856

Gnomad EAS AF: 0.749

Gnomad SAS AF: 0.875

Gnomad FIN AF: 0.791

Gnomad MID AF: 0.815

Gnomad NFE AF: 0.781

Gnomad OTH AF: 0.747

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

GnomAD4 genome AF: 0.745 AC: 113224 AN: 152016 Hom.: 42545 Cov.: 31 AF XY: 0.749 AC XY: 55628 AN XY: 74300

Gnomad4 AFR AF: 0.678

Gnomad4 AMR AF: 0.658

Gnomad4 ASJ AF: 0.856

Gnomad4 EAS AF: 0.749

Gnomad4 SAS AF: 0.876

Gnomad4 FIN AF: 0.791

Gnomad4 NFE AF: 0.781

Gnomad4 OTH AF: 0.747

Alfa AF: 0.764 Hom.: 5525

Bravo AF: 0.724

Asia WGS AF: 0.798 AC: 2775 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.76
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2352802; hg19: chr11-27547826;