chr10-14822888-T-A

Variant names:

• chr10-14822888-T-A
• rs1901650
• NM_001029954.3:c.385+2591A>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.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
• Publications: 2 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=-0.81).
• 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 rank	MANE	Protein	UniProt
CDNF	NM_001029954.3	c.385+2591A>T		intron_variant	Intron 3 of 3	ENST00000465530.2	NP_001025125.2
CDNF	XM_011519488.3	c.412+2564A>T		intron_variant	Intron 3 of 3		XP_011517790.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDNF	ENST00000465530.2	c.385+2591A>T		intron_variant	Intron 3 of 3	1	NM_001029954.3	ENSP00000419395.1

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

African (AFR) AF: 0.00149 AC: 62 AN: 41582

American (AMR) AF: 0.0612 AC: 936 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.00808 AC: 28 AN: 3464

East Asian (EAS) AF: 0.0820 AC: 425 AN: 5186

South Asian (SAS) AF: 0.0678 AC: 327 AN: 4826

European-Finnish (FIN) AF: 0.0220 AC: 233 AN: 10610

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00148 AC: 101 AN: 68022

Other (OTH) AF: 0.0109 AC: 23 AN: 2114

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
PhyloP100		0.045
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: rs1901650; hg19: chr10-14864887;