11-27645655-T-G

Position:

• chr11-27645655-T-G

Variant summary

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

The ENST00000499008.8(BDNF-AS):​n.374+5650T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.725 in 152,188 control chromosomes in the GnomAD database, including 40,207 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 0.72 (40207 hom., cov: 34)
• Consequence: BDNF-AS ENST00000499008.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.842

Genes affected

BDNF-AS (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.926 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BDNF-AS	NR_002832.2	n.374+5650T>G		intron_variant
BDNF-AS	NR_033312.1	n.305+5650T>G		intron_variant
BDNF-AS	NR_033313.1	n.305+5650T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BDNF-AS	ENST00000499008.8	n.374+5650T>G		intron_variant		1
BDNF-AS	ENST00000499568.3	n.305+5650T>G		intron_variant		1
BDNF-AS	ENST00000500662.7	n.305+5650T>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.725 AC: 110229 AN: 152070 Hom.: 40185 Cov.: 34

Gnomad AFR AF: 0.739

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.761

Gnomad ASJ AF: 0.830

Gnomad EAS AF: 0.948

Gnomad SAS AF: 0.653

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.700

Gnomad OTH AF: 0.730

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

GnomAD4 genome AF: 0.725 AC: 110298 AN: 152188 Hom.: 40207 Cov.: 34 AF XY: 0.726 AC XY: 54012 AN XY: 74402

Gnomad4 AFR AF: 0.739

Gnomad4 AMR AF: 0.761

Gnomad4 ASJ AF: 0.830

Gnomad4 EAS AF: 0.948

Gnomad4 SAS AF: 0.651

Gnomad4 FIN AF: 0.656

Gnomad4 NFE AF: 0.700

Gnomad4 OTH AF: 0.728

Alfa AF: 0.720 Hom.: 83492

Bravo AF: 0.735

Asia WGS AF: 0.739 AC: 2570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	11
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs925946; hg19: chr11-27667202;