rs879048

Positions:

• chr11-27617387-C-A
• chr11-27617387-C-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.145-22458C>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 0.736 in 152,018 control chromosomes in the GnomAD database, including 41,811 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 (41811 hom., cov: 31)
• Consequence: BDNF-AS NR_033312.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.420

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.79 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BDNF-AS	NR_033312.1	n.145-22458C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BDNF-AS	ENST00000651238.1	n.219-22458C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.736 AC: 111730 AN: 151898 Hom.: 41769 Cov.: 31

Gnomad AFR AF: 0.620

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.786

Gnomad ASJ AF: 0.729

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.737

Gnomad FIN AF: 0.840

Gnomad MID AF: 0.777

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.745

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

GnomAD4 genome AF: 0.736 AC: 111827 AN: 152018 Hom.: 41811 Cov.: 31 AF XY: 0.737 AC XY: 54791 AN XY: 74326

Gnomad4 AFR AF: 0.621

Gnomad4 AMR AF: 0.786

Gnomad4 ASJ AF: 0.729

Gnomad4 EAS AF: 0.518

Gnomad4 SAS AF: 0.738

Gnomad4 FIN AF: 0.840

Gnomad4 NFE AF: 0.795

Gnomad4 OTH AF: 0.745

Alfa AF: 0.762 Hom.: 6951

Bravo AF: 0.725

Asia WGS AF: 0.684 AC: 2381 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.46
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs879048; hg19: chr11-27638934;