10-14830428-C-A

Position:

• chr10-14830428-C-A

Variant summary

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

The NM_001029954.3(CDNF):​c.116-2156G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 152,070 control chromosomes in the GnomAD database, including 16,249 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 0.43 (16249 hom., cov: 32)
• Consequence: CDNF NM_001029954.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.904

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.676 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDNF	NM_001029954.3	c.116-2156G>T		intron_variant		ENST00000465530.2	NP_001025125.2
CDNF	XM_011519488.3	c.116-2156G>T		intron_variant			XP_011517790.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDNF	ENST00000465530.2	c.116-2156G>T		intron_variant		1	NM_001029954.3	ENSP00000419395	P1
CDNF	ENST00000378442.5	c.-191-2156G>T		intron_variant		1		ENSP00000367703
CDNF	ENST00000378441.6	n.136-2156G>T		intron_variant, non_coding_transcript_variant		2
CDNF	ENST00000466269.1	n.41-2156G>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65791 AN: 151950 Hom.: 16211 Cov.: 32

Gnomad AFR AF: 0.682

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.382

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.433 AC: 65887 AN: 152070 Hom.: 16249 Cov.: 32 AF XY: 0.425 AC XY: 31630 AN XY: 74358

Gnomad4 AFR AF: 0.682

Gnomad4 AMR AF: 0.424

Gnomad4 ASJ AF: 0.319

Gnomad4 EAS AF: 0.303

Gnomad4 SAS AF: 0.268

Gnomad4 FIN AF: 0.282

Gnomad4 NFE AF: 0.336

Gnomad4 OTH AF: 0.421

Alfa AF: 0.349 Hom.: 19286

Bravo AF: 0.458

Asia WGS AF: 0.329 AC: 1146 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.78
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7094179; hg19: chr10-14872427;