chr11-27541835-G-T

Position:

• chr11-27541835-G-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

BDNF-AS (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BDNF-AS	NR_002832.2	n.144+1719G>T		intron_variant
BDNF-AS	NR_033312.1	n.144+1719G>T		intron_variant
BDNF-AS	NR_033313.1	n.144+1719G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BDNF-AS	ENST00000499008.8	n.144+1719G>T		intron_variant		1
BDNF-AS	ENST00000499568.3	n.144+1719G>T		intron_variant		1
BDNF-AS	ENST00000500662.7	n.144+1719G>T		intron_variant		1

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

Gnomad4 AFR AF: 0.0479

Gnomad4 AMR AF: 0.255

Gnomad4 ASJ AF: 0.277

Gnomad4 EAS AF: 0.146

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.188

Gnomad4 NFE AF: 0.233

Gnomad4 OTH AF: 0.206

Alfa AF: 0.223 Hom.: 4736

Bravo AF: 0.179

Asia WGS AF: 0.192 AC: 663 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs988712; hg19: chr11-27563382;