ENST00000499008.8:n.214-12812A>G

Variant names:

• chr11-27627033-A-G
• rs4923457
• ENST00000499008.8:n.214-12812A>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000499008.8(BDNF-AS):​n.214-12812A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: BDNF-AS ENST00000499008.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890
• Publications: 14 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000499008.8. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BDNF-AS	NR_002832.2		n.214-12812A>G		intron	N/A
	BDNF-AS	NR_033312.1		n.145-12812A>G		intron	N/A
	BDNF-AS	NR_033313.1		n.145-12812A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BDNF-AS	ENST00000499008.8	TSL:1	n.214-12812A>G		intron	N/A
	BDNF-AS	ENST00000499568.3	TSL:1	n.145-12812A>G		intron	N/A
	BDNF-AS	ENST00000500662.7	TSL:1	n.145-12812A>G		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.7
DANN	Benign	0.64
PhyloP100		0.089

Splicing

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

Other links and lift over

dbSNP: rs4923457; hg19: chr11-27648580;