11-27648561-T-C

Variant names:

• chr11-27648561-T-C
• rs10501087
• ENST00000499008.8:n.374+8556T>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+8556T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 152,118 control chromosomes in the GnomAD database, including 2,967 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 0.17 (2967 hom., cov: 32)
• Consequence: BDNF-AS ENST00000499008.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.943
• Publications: 61 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.459 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BDNF-AS	NR_002832.2	n.374+8556T>C		intron_variant	Intron 4 of 7
BDNF-AS	NR_033312.1	n.305+8556T>C		intron_variant	Intron 3 of 8
BDNF-AS	NR_033313.1	n.305+8556T>C		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BDNF-AS	ENST00000499008.8	n.374+8556T>C		intron_variant	Intron 4 of 7	1
BDNF-AS	ENST00000499568.3	n.305+8556T>C		intron_variant	Intron 3 of 8	1
BDNF-AS	ENST00000500662.7	n.305+8556T>C		intron_variant	Intron 3 of 6	1

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26388 AN: 152002 Hom.: 2969 Cov.: 32

Gnomad AFR AF: 0.0646

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.173 AC: 26382 AN: 152118 Hom.: 2967 Cov.: 32 AF XY: 0.175 AC XY: 13029 AN XY: 74366

African (AFR) AF: 0.0644 AC: 2672 AN: 41514

American (AMR) AF: 0.180 AC: 2754 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 938 AN: 3464

East Asian (EAS) AF: 0.474 AC: 2454 AN: 5174

South Asian (SAS) AF: 0.264 AC: 1268 AN: 4812

European-Finnish (FIN) AF: 0.160 AC: 1687 AN: 10566

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.204 AC: 13838 AN: 67974

Other (OTH) AF: 0.191 AC: 402 AN: 2110

Alfa AF: 0.196 Hom.: 6128

Bravo AF: 0.172

Asia WGS AF: 0.298 AC: 1036 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.22
DANN	Benign	0.59
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs10501087; hg19: chr11-27670108;