rs3808871

Variant names:

• chr9-34591427-G-A
• rs3808871
• ENST00000868690.1:c.-112+1913C>T

Variant summary

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

The ENST00000868690.1(CNTFR):​c.-112+1913C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.22 in 152,280 control chromosomes in the GnomAD database, including 3,889 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 0.22 (3889 hom., cov: 33)
• Consequence: CNTFR ENST00000868690.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.684
• Publications: 5 publications found

Genes affected

CNTFR (HGNC:2170): (ciliary neurotrophic factor receptor) This gene encodes a member of the type 1 cytokine receptor family. The encoded protein is the ligand-specific component of a tripartite receptor for ciliary neurotrophic factor, which plays a critical role in neuronal cell survival, differentiation and gene expression. Binding of ciliary neurotrophic factor to the encoded protein recruits the transmembrane components of the receptor, gp130 and leukemia inhibitory factor receptor, facilitating signal transduction. Single nucleotide polymorphisms in this gene may be associated with variations in muscle strength, as well as early onset of eating disorders. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, May 2011]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000868690.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CNTFR	ENST00000868690.1		c.-112+1913C>T		intron	N/A	ENSP00000538749.1
	CNTFR	ENST00000868691.1		c.-112+124C>T		intron	N/A	ENSP00000538750.1

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33399 AN: 152162 Hom.: 3882 Cov.: 33

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.220 AC: 33437 AN: 152280 Hom.: 3889 Cov.: 33 AF XY: 0.220 AC XY: 16392 AN XY: 74458

African (AFR) AF: 0.151 AC: 6286 AN: 41578

American (AMR) AF: 0.273 AC: 4183 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 885 AN: 3468

East Asian (EAS) AF: 0.148 AC: 767 AN: 5188

South Asian (SAS) AF: 0.244 AC: 1179 AN: 4832

European-Finnish (FIN) AF: 0.227 AC: 2409 AN: 10604

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.250 AC: 16990 AN: 67990

Other (OTH) AF: 0.211 AC: 447 AN: 2116

Alfa AF: 0.242 Hom.: 611

Bravo AF: 0.220

Asia WGS AF: 0.173 AC: 602 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	8.7
DANN	Benign	0.84
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs3808871; hg19: chr9-34591425;