chr11-27541835-G-T

Variant names:

• chr11-27541835-G-T
• rs988712
• ENST00000499008.8:n.144+1719G>T

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+1719G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 152,002 control chromosomes in the GnomAD database, including 3,151 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 0.18 (3151 hom., cov: 32)
• Consequence: BDNF-AS ENST00000499008.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.425
• Publications: 38 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=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.261 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BDNF-AS	NR_002832.2		n.144+1719G>T		intron	N/A
	BDNF-AS	NR_033312.1		n.144+1719G>T		intron	N/A
	BDNF-AS	NR_033313.1		n.144+1719G>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BDNF-AS	ENST00000499008.8	TSL:1	n.144+1719G>T		intron	N/A
	BDNF-AS	ENST00000499568.3	TSL:1	n.144+1719G>T		intron	N/A
	BDNF-AS	ENST00000500662.7	TSL:1	n.144+1719G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27562 AN: 151884 Hom.: 3153 Cov.: 32

Gnomad AFR AF: 0.0480

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.181 AC: 27556 AN: 152002 Hom.: 3151 Cov.: 32 AF XY: 0.182 AC XY: 13525 AN XY: 74306

African (AFR) AF: 0.0479 AC: 1989 AN: 41544

American (AMR) AF: 0.255 AC: 3886 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.277 AC: 960 AN: 3464

East Asian (EAS) AF: 0.146 AC: 756 AN: 5162

South Asian (SAS) AF: 0.273 AC: 1315 AN: 4820

European-Finnish (FIN) AF: 0.188 AC: 1988 AN: 10564

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.233 AC: 15843 AN: 67900

Other (OTH) AF: 0.206 AC: 434 AN: 2108

Alfa AF: 0.217 Hom.: 11873

Bravo AF: 0.179

Asia WGS AF: 0.192 AC: 663 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.091
DANN	Benign	0.33
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs988712; hg19: chr11-27563382;