rs35258303

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.196
Variant links:
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
CDNFNM_001029954.3 linkuse as main transcriptc.115+2946C>T intron_variant ENST00000465530.2 NP_001025125.2
CDNFXM_011519488.3 linkuse as main transcriptc.115+2946C>T intron_variant XP_011517790.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CDNFENST00000465530.2 linkuse as main transcriptc.115+2946C>T intron_variant 1 NM_001029954.3 ENSP00000419395 P1Q49AH0-1
CDNFENST00000378442.5 linkuse as main transcriptc.-308-553C>T intron_variant 1 ENSP00000367703 Q49AH0-2
CDNFENST00000378441.6 linkuse as main transcriptn.135+1365C>T intron_variant, non_coding_transcript_variant 2
CDNFENST00000466269.1 linkuse as main transcriptn.40+1365C>T intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.113
AC:
17215
AN:
152086
Hom.:
1117
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0679
Gnomad AMI
AF:
0.126
Gnomad AMR
AF:
0.109
Gnomad ASJ
AF:
0.0963
Gnomad EAS
AF:
0.00577
Gnomad SAS
AF:
0.102
Gnomad FIN
AF:
0.148
Gnomad MID
AF:
0.120
Gnomad NFE
AF:
0.146
Gnomad OTH
AF:
0.104
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.113
AC:
17225
AN:
152204
Hom.:
1117
Cov.:
32
AF XY:
0.113
AC XY:
8411
AN XY:
74406
show subpopulations
Gnomad4 AFR
AF:
0.0680
Gnomad4 AMR
AF:
0.109
Gnomad4 ASJ
AF:
0.0963
Gnomad4 EAS
AF:
0.00598
Gnomad4 SAS
AF:
0.101
Gnomad4 FIN
AF:
0.148
Gnomad4 NFE
AF:
0.146
Gnomad4 OTH
AF:
0.105
Alfa
AF:
0.133
Hom.:
1413
Bravo
AF:
0.107
Asia WGS
AF:
0.0590
AC:
209
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
2.4
DANN
Benign
0.33

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs35258303; hg19: chr10-14876885; API