rs1901650

chr10-14822888-T-A

Variant summary

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

The NM_001029954.3(CDNF):c.385+2591A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.014 in 152,304 control chromosomes in the GnomAD database, including 87 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 0.014 (87 hom., cov: 32)
• Consequence: CDNF NM_001029954.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0450

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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0755 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDNF	NM_001029954.3	c.385+2591A>T		intron_variant		ENST00000465530.2
CDNF	XM_011519488.3	c.412+2564A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDNF	ENST00000465530.2	c.385+2591A>T		intron_variant		1	NM_001029954.3	P1

Frequencies

GnomAD3 genomes AF: 0.0141 AC: 2139 AN: 152186 Hom.: 89 Cov.: 32

Gnomad AFR AF: 0.00150

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0610

Gnomad ASJ AF: 0.00808

Gnomad EAS AF: 0.0820

Gnomad SAS AF: 0.0685

Gnomad FIN AF: 0.0220

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00148

Gnomad OTH AF: 0.0124

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

GnomAD4 genome AF: 0.0140 AC: 2135 AN: 152304 Hom.: 87 Cov.: 32 AF XY: 0.0169 AC XY: 1261 AN XY: 74472

Gnomad4 AFR AF: 0.00149

Gnomad4 AMR AF: 0.0612

Gnomad4 ASJ AF: 0.00808

Gnomad4 EAS AF: 0.0820

Gnomad4 SAS AF: 0.0678

Gnomad4 FIN AF: 0.0220

Gnomad4 NFE AF: 0.00148

Gnomad4 OTH AF: 0.0109

Alfa AF: 0.00693 Hom.: 2

Bravo AF: 0.0161

Asia WGS AF: 0.0820 AC: 284 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	5.2
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1901650; hg19: chr10-14864887;