10-14834886-G-A

Position:

• chr10-14834886-G-A

Variant summary

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

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
• 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]

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 (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: 17215 AN: 152086 Hom.: 1117 Cov.: 32

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

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

Other links and lift over

dbSNP: rs35258303; hg19: chr10-14876885;