rs7900873

Variant names:

• chr10-14821865-G-A
• rs7900873
• NM_001029954.3:c.386-1707C>T

Your query was ambiguous. Multiple possible variants found:

• chr10-14821865-G-A
• chr10-14821865-G-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.386-1707C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 151,980 control chromosomes in the GnomAD database, including 14,673 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 0.40 (14673 hom., cov: 32)
• Consequence: CDNF NM_001029954.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.287
• Publications: 10 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.677 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001029954.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDNF	NM_001029954.3	MANE Select	c.386-1707C>T		intron	N/A	NP_001025125.2	Q49AH0-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDNF	ENST00000465530.2	TSL:1 MANE Select	c.386-1707C>T		intron	N/A	ENSP00000419395.1	Q49AH0-1
	CDNF	ENST00000378442.5	TSL:1	c.80-1707C>T		intron	N/A	ENSP00000367703.1	Q49AH0-2
	CDNF	ENST00000861566.1		c.116-1707C>T		intron	N/A	ENSP00000531625.1

Frequencies

GnomAD3 genomes AF: 0.399 AC: 60638 AN: 151860 Hom.: 14630 Cov.: 32

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.400 AC: 60740 AN: 151980 Hom.: 14673 Cov.: 32 AF XY: 0.401 AC XY: 29761 AN XY: 74304

African (AFR) AF: 0.684 AC: 28309 AN: 41414

American (AMR) AF: 0.356 AC: 5431 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.336 AC: 1166 AN: 3468

East Asian (EAS) AF: 0.337 AC: 1744 AN: 5170

South Asian (SAS) AF: 0.468 AC: 2258 AN: 4828

European-Finnish (FIN) AF: 0.234 AC: 2472 AN: 10550

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.267 AC: 18153 AN: 67974

Other (OTH) AF: 0.352 AC: 744 AN: 2114

Alfa AF: 0.307 Hom.: 34918

Bravo AF: 0.417

Asia WGS AF: 0.389 AC: 1356 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.0
DANN	Benign	0.52
PhyloP100		0.29
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: rs7900873; hg19: chr10-14863864;