11-27643996-T-C

Variant names:

• chr11-27643996-T-C
• rs11030096
• ENST00000499008.8:n.374+3991T>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.374+3991T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 152,124 control chromosomes in the GnomAD database, including 11,917 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 0.37 (11917 hom., cov: 33)
• Consequence: BDNF-AS ENST00000499008.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.123
• Publications: 21 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.475 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000499008.8. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BDNF-AS	NR_002832.2		n.374+3991T>C		intron	N/A
	BDNF-AS	NR_033312.1		n.305+3991T>C		intron	N/A
	BDNF-AS	NR_033313.1		n.305+3991T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BDNF-AS	ENST00000499008.8	TSL:1	n.374+3991T>C		intron	N/A
	BDNF-AS	ENST00000499568.3	TSL:1	n.305+3991T>C		intron	N/A
	BDNF-AS	ENST00000500662.7	TSL:1	n.305+3991T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56188 AN: 152008 Hom.: 11920 Cov.: 33

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.369 AC: 56185 AN: 152124 Hom.: 11917 Cov.: 33 AF XY: 0.369 AC XY: 27458 AN XY: 74374

African (AFR) AF: 0.172 AC: 7142 AN: 41552

American (AMR) AF: 0.327 AC: 5001 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.512 AC: 1777 AN: 3472

East Asian (EAS) AF: 0.306 AC: 1585 AN: 5180

South Asian (SAS) AF: 0.319 AC: 1538 AN: 4818

European-Finnish (FIN) AF: 0.489 AC: 5161 AN: 10552

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.480 AC: 32589 AN: 67962

Other (OTH) AF: 0.398 AC: 838 AN: 2108

Alfa AF: 0.431 Hom.: 21857

Bravo AF: 0.347

Asia WGS AF: 0.307 AC: 1069 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.8
DANN	Benign	0.61
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs11030096; hg19: chr11-27665543;