rs7094179

Variant names:

• chr10-14830428-C-A
• rs7094179
• NM_001029954.3:c.116-2156G>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CDNF	NM_001029954.3	c.116-2156G>T		intron_variant	Intron 1 of 3	ENST00000465530.2	NP_001025125.2
CDNF	XM_011519488.3	c.116-2156G>T		intron_variant	Intron 1 of 3		XP_011517790.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDNF	ENST00000465530.2	c.116-2156G>T		intron_variant	Intron 1 of 3	1	NM_001029954.3	ENSP00000419395.1
CDNF	ENST00000378442.5	c.-191-2156G>T		intron_variant	Intron 3 of 5	1		ENSP00000367703.1
CDNF	ENST00000378441.6	n.136-2156G>T		intron_variant	Intron 2 of 3	2
CDNF	ENST00000466269.1	n.41-2156G>T		intron_variant	Intron 1 of 3	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

African (AFR) AF: 0.682 AC: 28296 AN: 41470

American (AMR) AF: 0.424 AC: 6474 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 1107 AN: 3472

East Asian (EAS) AF: 0.303 AC: 1563 AN: 5158

South Asian (SAS) AF: 0.268 AC: 1294 AN: 4820

European-Finnish (FIN) AF: 0.282 AC: 2980 AN: 10580

Middle Eastern (MID) AF: 0.387 AC: 113 AN: 292

European-Non Finnish (NFE) AF: 0.336 AC: 22868 AN: 67980

Other (OTH) AF: 0.421 AC: 886 AN: 2106

Alfa AF: 0.363 Hom.: 45737

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
PhyloP100		-0.90
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs7094179; hg19: chr10-14872427;