chr10-14819402-C-T

Variant names:

• chr10-14819402-C-T
• rs2278871
• NM_001029954.3:c.*578G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001029954.3(CDNF):​c.*578G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 152,072 control chromosomes in the GnomAD database, including 3,150 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 0.18 (3150 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CDNF NM_001029954.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.194
• Publications: 5 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=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDNF	NM_001029954.3	c.*578G>A		3_prime_UTR_variant	Exon 4 of 4	ENST00000465530.2	NP_001025125.2
CDNF	XM_011519488.3	c.*578G>A		3_prime_UTR_variant	Exon 4 of 4		XP_011517790.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDNF	ENST00000465530.2	c.*578G>A		3_prime_UTR_variant	Exon 4 of 4	1	NM_001029954.3	ENSP00000419395.1
CDNF	ENST00000378442.5	c.*578G>A		3_prime_UTR_variant	Exon 6 of 6	1		ENSP00000367703.1
CDNF	ENST00000378441.6	n.*129G>A		downstream_gene_variant		2

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26583 AN: 151954 Hom.: 3138 Cov.: 32

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.0564

Gnomad MID AF: 0.191

Gnomad NFE AF: 0.0965

Gnomad OTH AF: 0.165

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 4

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 6

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.175 AC: 26641 AN: 152072 Hom.: 3150 Cov.: 32 AF XY: 0.177 AC XY: 13186 AN XY: 74342

African (AFR) AF: 0.307 AC: 12712 AN: 41452

American (AMR) AF: 0.144 AC: 2203 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 698 AN: 3468

East Asian (EAS) AF: 0.319 AC: 1653 AN: 5178

South Asian (SAS) AF: 0.337 AC: 1623 AN: 4814

European-Finnish (FIN) AF: 0.0564 AC: 596 AN: 10572

Middle Eastern (MID) AF: 0.195 AC: 57 AN: 292

European-Non Finnish (NFE) AF: 0.0965 AC: 6560 AN: 67982

Other (OTH) AF: 0.164 AC: 346 AN: 2116

Alfa AF: 0.117 Hom.: 1747

Bravo AF: 0.184

Asia WGS AF: 0.288 AC: 1002 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.83
DANN	Benign	0.53
PhyloP100		-0.19
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: rs2278871; hg19: chr10-14861401;