rs61888800

Variant names:

• chr11-27700731-G-C
• rs61888800
• ENST00000530861.5:c.-77C>G

Your query was ambiguous. Multiple possible variants found:

• chr11-27700731-G-C
• chr11-27700731-G-T

Variant summary

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

The NM_001143812.2(BDNF):​c.-77C>G variant causes a 5 prime UTR 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)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: BDNF NM_001143812.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700
• Publications: 24 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: 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=-0.81).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001143812.2. 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_001143812.2		c.-77C>G		5_prime_UTR	Exon 1 of 2	NP_001137284.1	A0A0E3SU01
	BDNF	NM_001143810.2		c.-59+240C>G		intron	N/A	NP_001137282.1	P23560-4
	BDNF	NM_001143809.2		c.66+240C>G		intron	N/A	NP_001137281.1	P23560-5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BDNF	ENST00000530861.5	TSL:1	c.-77C>G		5_prime_UTR	Exon 1 of 2	ENSP00000435564.1	P23560-1
	BDNF	ENST00000438929.5	TSL:1	c.-59+240C>G		intron	N/A	ENSP00000414303.1	P23560-4
	BDNF	ENST00000314915.6	TSL:1	c.3+20681C>G		intron	N/A	ENSP00000320002.6	P23560-2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1032648 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 494054

African (AFR) AF: 0.00 AC: 0 AN: 20924

American (AMR) AF: 0.00 AC: 0 AN: 12104

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 9582

East Asian (EAS) AF: 0.00 AC: 0 AN: 11998

South Asian (SAS) AF: 0.00 AC: 0 AN: 57840

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 9182

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2284

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 871868

Other (OTH) AF: 0.00 AC: 0 AN: 36866

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 337

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.5
DANN	Benign	0.82
PhyloP100		0.0070
PromoterAI		0.037	Neutral

Splicing

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

Other links and lift over

dbSNP: rs61888800; hg19: chr11-27722278;