11-27507440-A-T

Variant names:

• chr11-27507440-A-T
• rs3763965
• ENST00000499008.8:n.47+542A>T

Variant summary

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

The ENST00000652425.1(BDNF-AS):​n.566A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 152,128 control chromosomes in the GnomAD database, including 15,919 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 0.42 (15919 hom., cov: 33)
• Consequence: BDNF-AS ENST00000652425.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00800
• Publications: 6 publications found

Genes affected

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

LGR4-AS1 (HGNC:40629): (LGR4 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.553 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000652425.1. 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.47+542A>T		intron	N/A
	BDNF-AS	NR_033312.1		n.47+542A>T		intron	N/A
	BDNF-AS	NR_033313.1		n.47+542A>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BDNF-AS	ENST00000499008.8	TSL:1	n.47+542A>T		intron	N/A
	BDNF-AS	ENST00000499568.3	TSL:1	n.47+542A>T		intron	N/A
	BDNF-AS	ENST00000500662.7	TSL:1	n.47+542A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.419 AC: 63754 AN: 152010 Hom.: 15915 Cov.: 33

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.567

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.419 AC: 63745 AN: 152128 Hom.: 15919 Cov.: 33 AF XY: 0.422 AC XY: 31362 AN XY: 74354

African (AFR) AF: 0.149 AC: 6185 AN: 41536

American (AMR) AF: 0.354 AC: 5412 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1916 AN: 3470

East Asian (EAS) AF: 0.434 AC: 2243 AN: 5172

South Asian (SAS) AF: 0.528 AC: 2545 AN: 4824

European-Finnish (FIN) AF: 0.567 AC: 5979 AN: 10544

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

European-Non Finnish (NFE) AF: 0.558 AC: 37900 AN: 67974

Other (OTH) AF: 0.430 AC: 909 AN: 2112

Alfa AF: 0.362 Hom.: 1219

Bravo AF: 0.386

Asia WGS AF: 0.475 AC: 1652 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.2
DANN	Benign	0.75
PhyloP100		-0.0080

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3763965;

hg19: chr11-27528987;