11-27561582-T-C

Variant names:

• chr11-27561582-T-C
• rs7481311
• ENST00000499008.8:n.144+21466T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000499008.8(BDNF-AS):​n.144+21466T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.749 in 152,094 control chromosomes in the GnomAD database, including 43,013 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 0.75 (43013 hom., cov: 32)
• Consequence: BDNF-AS ENST00000499008.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00600
• Publications: 30 publications found

Genes affected

BDNF-AS (HGNC:20608): (BDNF antisense RNA)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• 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 rank	MANE	Protein	UniProt
BDNF-AS	NR_002832.2	n.144+21466T>C		intron_variant	Intron 2 of 7
BDNF-AS	NR_033312.1	n.144+21466T>C		intron_variant	Intron 2 of 8
BDNF-AS	NR_033313.1	n.144+21466T>C		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BDNF-AS	ENST00000499008.8	n.144+21466T>C		intron_variant	Intron 2 of 7	1
BDNF-AS	ENST00000499568.3	n.144+21466T>C		intron_variant	Intron 2 of 8	1
BDNF-AS	ENST00000500662.7	n.144+21466T>C		intron_variant	Intron 2 of 6	1

Frequencies

GnomAD3 genomes AF: 0.749 AC: 113782 AN: 151976 Hom.: 42982 Cov.: 32

Gnomad AFR AF: 0.692

Gnomad AMI AF: 0.821

Gnomad AMR AF: 0.663

Gnomad ASJ AF: 0.875

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.875

Gnomad FIN AF: 0.791

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.779

Gnomad OTH AF: 0.749

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

GnomAD4 genome AF: 0.749 AC: 113854 AN: 152094 Hom.: 43013 Cov.: 32 AF XY: 0.752 AC XY: 55894 AN XY: 74348

African (AFR) AF: 0.692 AC: 28680 AN: 41462

American (AMR) AF: 0.661 AC: 10106 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.875 AC: 3038 AN: 3472

East Asian (EAS) AF: 0.753 AC: 3899 AN: 5180

South Asian (SAS) AF: 0.876 AC: 4225 AN: 4822

European-Finnish (FIN) AF: 0.791 AC: 8372 AN: 10580

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.779 AC: 52959 AN: 67978

Other (OTH) AF: 0.749 AC: 1581 AN: 2112

Alfa AF: 0.770 Hom.: 164373

Bravo AF: 0.729

Asia WGS AF: 0.802 AC: 2790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.3
DANN	Benign	0.42
PhyloP100		-0.0060

Splicing

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

Other links and lift over

dbSNP: rs7481311; hg19: chr11-27583129;