ENST00000314915.6:c.3+19896C>T

Variant names:

• chr11-27701516-G-A
• rs11030118
• ENST00000314915.6:c.3+19896C>T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The ENST00000314915.6(BDNF):​c.3+19896C>T variant causes a intron change. 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)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: BDNF ENST00000314915.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.61
• Publications: 5 publications found

Genes affected

BDNF (HGNC:1033): (brain derived neurotrophic factor) This gene encodes a member of the nerve growth factor family of proteins. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein that is proteolytically processed to generate the mature protein. Binding of this protein to its cognate receptor promotes neuronal survival in the adult brain. Expression of this gene is reduced in Alzheimer's, Parkinson's, and Huntington's disease patients. This gene may play a role in the regulation of the stress response and in the biology of mood disorders. [provided by RefSeq, Nov 2015]

ENSG00000255496 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000314915.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BDNF	NM_170733.4		c.-241C>T		5_prime_UTR	Exon 1 of 2	NP_733929.1	A0A0E3SU01
	BDNF	NM_170731.5		c.3+19896C>T		intron	N/A	NP_733927.1	P23560-2
	BDNF	NM_001143805.1		c.-22+19128C>T		intron	N/A	NP_001137277.1	P23560-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BDNF	ENST00000314915.6	TSL:1	c.3+19896C>T		intron	N/A	ENSP00000320002.6	P23560-2
	BDNF	ENST00000395978.7	TSL:1	c.-22+18913C>T		intron	N/A	ENSP00000379302.3	P23560-1
	BDNF	ENST00000395981.7	TSL:1	c.-22+18830C>T		intron	N/A	ENSP00000379305.3	P23560-1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 836158 Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0 AN XY: 386316

African (AFR) AF: 0.00 AC: 0 AN: 15828

American (AMR) AF: 0.00 AC: 0 AN: 1460

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 5200

East Asian (EAS) AF: 0.00 AC: 0 AN: 3794

South Asian (SAS) AF: 0.00 AC: 0 AN: 16710

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 370

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1630

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 763768

Other (OTH) AF: 0.00 AC: 0 AN: 27398

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	20
DANN	Benign	0.93
PhyloP100		4.6
PromoterAI		0.19	Neutral

Splicing

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

Other links and lift over

dbSNP: rs11030118; hg19: chr11-27723063;