rs4074134

Variant names:

• chr11-27625738-C-T
• rs4074134
• ENST00000499008.8:n.214-14107C>T

Variant summary

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

The ENST00000499008.8(BDNF-AS):​n.214-14107C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 152,068 control chromosomes in the GnomAD database, including 3,382 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 0.20 (3382 hom., cov: 32)
• Consequence: BDNF-AS ENST00000499008.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.322
• Publications: 40 publications found

Genes affected

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

LINC00678 (HGNC:44413): (long intergenic non-protein coding RNA 678)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.426 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BDNF-AS	NR_002832.2	n.214-14107C>T		intron_variant	Intron 3 of 7
BDNF-AS	NR_033312.1	n.145-14107C>T		intron_variant	Intron 2 of 8
BDNF-AS	NR_033313.1	n.145-14107C>T		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BDNF-AS	ENST00000499008.8	n.214-14107C>T		intron_variant	Intron 3 of 7	1
BDNF-AS	ENST00000499568.3	n.145-14107C>T		intron_variant	Intron 2 of 8	1
BDNF-AS	ENST00000500662.7	n.145-14107C>T		intron_variant	Intron 2 of 6	1

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30669 AN: 151950 Hom.: 3378 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.202 AC: 30688 AN: 152068 Hom.: 3382 Cov.: 32 AF XY: 0.202 AC XY: 15053 AN XY: 74342

African (AFR) AF: 0.167 AC: 6942 AN: 41482

American (AMR) AF: 0.191 AC: 2924 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 937 AN: 3470

East Asian (EAS) AF: 0.441 AC: 2272 AN: 5148

South Asian (SAS) AF: 0.266 AC: 1279 AN: 4806

European-Finnish (FIN) AF: 0.160 AC: 1694 AN: 10572

Middle Eastern (MID) AF: 0.223 AC: 65 AN: 292

European-Non Finnish (NFE) AF: 0.204 AC: 13835 AN: 67984

Other (OTH) AF: 0.205 AC: 434 AN: 2114

Alfa AF: 0.210 Hom.: 11040

Bravo AF: 0.205

Asia WGS AF: 0.293 AC: 1019 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.55
DANN	Benign	0.38
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs4074134; hg19: chr11-27647285;