rs56164415
Positions:
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The NM_001709.5(BDNF):c.-46C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0625 in 985,630 control chromosomes in the GnomAD database, including 2,438 homozygotes. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Genomes: 𝑓 0.061 ( 400 hom., cov: 32)
Exomes 𝑓: 0.063 ( 2038 hom. )
Consequence
BDNF
NM_001709.5 5_prime_UTR
NM_001709.5 5_prime_UTR
Scores
1
1
Clinical Significance
Conservation
PhyloP100: 2.49
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BDNF | NM_001709.5 | c.-46C>T | 5_prime_UTR_variant | 1/2 | ENST00000356660.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BDNF | ENST00000356660.9 | c.-46C>T | 5_prime_UTR_variant | 1/2 | 1 | NM_001709.5 | P4 | ||
ENST00000530663.1 | n.148-3666C>T | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0609 AC: 9264AN: 152076Hom.: 396 Cov.: 32
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?
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GnomAD4 exome AF: 0.0628 AC: 52326AN: 833438Hom.: 2038 Cov.: 28 AF XY: 0.0637 AC XY: 24503AN XY: 384956
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GnomAD4 genome ? AF: 0.0611 AC: 9294AN: 152192Hom.: 400 Cov.: 32 AF XY: 0.0664 AC XY: 4943AN XY: 74406
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Variant of unknown significance Uncertain:1
Uncertain significance, no assertion criteria provided | literature only | OMIM | Jun 15, 2004 | - - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Uncertain
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at