rs35258303
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001029954.3(CDNF):c.115+2946C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 152,204 control chromosomes in the GnomAD database, including 1,117 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 0.11 ( 1117 hom., cov: 32)
Consequence
CDNF
NM_001029954.3 intron
NM_001029954.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.196
Genes affected
CDNF (HGNC:24913): (cerebral dopamine neurotrophic factor) Predicted to enable growth factor activity. Predicted to be involved in dopaminergic neuron differentiation and neuron projection development. Predicted to be active in endoplasmic reticulum and extracellular space. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CDNF | NM_001029954.3 | c.115+2946C>T | intron_variant | ENST00000465530.2 | NP_001025125.2 | |||
CDNF | XM_011519488.3 | c.115+2946C>T | intron_variant | XP_011517790.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CDNF | ENST00000465530.2 | c.115+2946C>T | intron_variant | 1 | NM_001029954.3 | ENSP00000419395 | P1 | |||
CDNF | ENST00000378442.5 | c.-308-553C>T | intron_variant | 1 | ENSP00000367703 | |||||
CDNF | ENST00000378441.6 | n.135+1365C>T | intron_variant, non_coding_transcript_variant | 2 | ||||||
CDNF | ENST00000466269.1 | n.40+1365C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.113 AC: 17215AN: 152086Hom.: 1117 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.113 AC: 17225AN: 152204Hom.: 1117 Cov.: 32 AF XY: 0.113 AC XY: 8411AN XY: 74406
GnomAD4 genome
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209
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at