11-27578611-G-C

Variant names:

• chr11-27578611-G-C
• rs1387145
• ENST00000499008.8:n.145-5658G>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.145-5658G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 151,732 control chromosomes in the GnomAD database, including 14,677 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 0.40 (14677 hom., cov: 31)
• Consequence: BDNF-AS ENST00000499008.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.87
• Publications: 2 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=-1.08).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.527 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BDNF-AS	NR_002832.2	n.145-5658G>C		intron_variant	Intron 2 of 7
BDNF-AS	NR_033312.1	n.144+38495G>C		intron_variant	Intron 2 of 8
BDNF-AS	NR_033313.1	n.144+38495G>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.145-5658G>C		intron_variant	Intron 2 of 7	1
BDNF-AS	ENST00000499568.3	n.144+38495G>C		intron_variant	Intron 2 of 8	1
BDNF-AS	ENST00000500662.7	n.144+38495G>C		intron_variant	Intron 2 of 6	1

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61300 AN: 151612 Hom.: 14676 Cov.: 31

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.404 AC: 61290 AN: 151732 Hom.: 14677 Cov.: 31 AF XY: 0.408 AC XY: 30275 AN XY: 74124

African (AFR) AF: 0.148 AC: 6112 AN: 41394

American (AMR) AF: 0.337 AC: 5129 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.540 AC: 1870 AN: 3466

East Asian (EAS) AF: 0.431 AC: 2191 AN: 5086

South Asian (SAS) AF: 0.524 AC: 2516 AN: 4804

European-Finnish (FIN) AF: 0.564 AC: 5926 AN: 10508

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.531 AC: 36080 AN: 67918

Other (OTH) AF: 0.414 AC: 874 AN: 2112

Alfa AF: 0.469 Hom.: 2353

Bravo AF: 0.370

Asia WGS AF: 0.477 AC: 1658 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.18
DANN	Benign	0.40
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs1387145; hg19: chr11-27600158;