chr10-14821865-G-A

Position:

• chr10-14821865-G-A

Variant summary

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

The ENST00000465530.2(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 ENST00000465530.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.287

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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.677 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDNF	NM_001029954.3	c.386-1707C>T		intron_variant		ENST00000465530.2	NP_001025125.2
CDNF	XM_011519488.3	c.413-1707C>T		intron_variant			XP_011517790.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDNF	ENST00000465530.2	c.386-1707C>T		intron_variant		1	NM_001029954.3	ENSP00000419395	P1

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

Gnomad4 AFR AF: 0.684

Gnomad4 AMR AF: 0.356

Gnomad4 ASJ AF: 0.336

Gnomad4 EAS AF: 0.337

Gnomad4 SAS AF: 0.468

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.352

Alfa AF: 0.289 Hom.: 13999

Bravo AF: 0.417

Asia WGS AF: 0.389 AC: 1356 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.0
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7900873; hg19: chr10-14863864;