rs11259365

chr10-14834528-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001029954.3(CDNF):c.115+3304C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0918 in 152,070 control chromosomes in the GnomAD database, including 1,158 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 0.092 (1158 hom., cov: 32)
• Consequence: CDNF NM_001029954.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.863

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDNF	NM_001029954.3	c.115+3304C>G		intron_variant		ENST00000465530.2
CDNF	XM_011519488.3	c.115+3304C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDNF	ENST00000465530.2	c.115+3304C>G		intron_variant		1	NM_001029954.3	P1
CDNF	ENST00000378442.5	c.-308-195C>G		intron_variant		1
CDNF	ENST00000378441.6	n.135+1723C>G		intron_variant, non_coding_transcript_variant		2
CDNF	ENST00000466269.1	n.40+1723C>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0916 AC: 13921 AN: 151948 Hom.: 1154 Cov.: 32

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.0647

Gnomad ASJ AF: 0.0372

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.0150

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0297

Gnomad OTH AF: 0.0805

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0918 AC: 13954 AN: 152070 Hom.: 1158 Cov.: 32 AF XY: 0.0930 AC XY: 6912 AN XY: 74362

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.0650

Gnomad4 ASJ AF: 0.0372

Gnomad4 EAS AF: 0.270

Gnomad4 SAS AF: 0.130

Gnomad4 FIN AF: 0.0150

Gnomad4 NFE AF: 0.0298

Gnomad4 OTH AF: 0.0801

Alfa AF: 0.0629 Hom.: 76

Bravo AF: 0.0998

Asia WGS AF: 0.174 AC: 604 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	5.3
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11259365; hg19: chr10-14876527;