rs1304100

Variant names:

• chr11-27550056-A-G
• rs1304100
• ENST00000499008.8:n.144+9940A>G

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+9940A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 152,102 control chromosomes in the GnomAD database, including 6,602 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 0.28 (6602 hom., cov: 32)
• Consequence: BDNF-AS ENST00000499008.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.152
• Publications: 11 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=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BDNF-AS	NR_002832.2	n.144+9940A>G		intron_variant	Intron 2 of 7
BDNF-AS	NR_033312.1	n.144+9940A>G		intron_variant	Intron 2 of 8
BDNF-AS	NR_033313.1	n.144+9940A>G		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BDNF-AS	ENST00000499008.8	n.144+9940A>G		intron_variant	Intron 2 of 7	1
BDNF-AS	ENST00000499568.3	n.144+9940A>G		intron_variant	Intron 2 of 8	1
BDNF-AS	ENST00000500662.7	n.144+9940A>G		intron_variant	Intron 2 of 6	1

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42874 AN: 151984 Hom.: 6599 Cov.: 32

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.282 AC: 42893 AN: 152102 Hom.: 6602 Cov.: 32 AF XY: 0.279 AC XY: 20785 AN XY: 74370

African (AFR) AF: 0.398 AC: 16498 AN: 41490

American (AMR) AF: 0.294 AC: 4488 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 964 AN: 3468

East Asian (EAS) AF: 0.146 AC: 757 AN: 5170

South Asian (SAS) AF: 0.274 AC: 1317 AN: 4814

European-Finnish (FIN) AF: 0.190 AC: 2012 AN: 10590

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.234 AC: 15875 AN: 67972

Other (OTH) AF: 0.283 AC: 597 AN: 2110

Alfa AF: 0.258 Hom.: 11843

Bravo AF: 0.294

Asia WGS AF: 0.212 AC: 738 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	4.9
DANN	Benign	0.92
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs1304100; hg19: chr11-27571603;