rs1304100

Positions:

• chr11-27550056-A-G

Variant summary

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

The NR_033312.1(BDNF-AS):​n.144+9940A>G 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 0.282 in 152,102 control chromosomes in the GnomAD database, including 6,602 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 0.28 (6602 hom., cov: 32)
• Consequence: BDNF-AS NR_033312.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.152

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=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BDNF-AS	NR_033312.1	n.144+9940A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BDNF-AS	ENST00000651238.1	n.149+9940A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42874 AN: 151984 Hom.: 6599 Cov.: 32

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.282 AC: 42893 AN: 152102 Hom.: 6602 Cov.: 32 AF XY: 0.279 AC XY: 20785 AN XY: 74370

Gnomad4 AFR AF: 0.398

Gnomad4 AMR AF: 0.294

Gnomad4 ASJ AF: 0.278

Gnomad4 EAS AF: 0.146

Gnomad4 SAS AF: 0.274

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.234

Gnomad4 OTH AF: 0.283

Alfa AF: 0.255 Hom.: 4178

Bravo AF: 0.294

Asia WGS AF: 0.212 AC: 738 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	4.9
DANN	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1304100; hg19: chr11-27571603;