rs41274853

Variant names:

• chr9-34551898-G-A
• rs41274853
• NM_147164.3:c.*173C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-34551898-G-A
• chr9-34551898-G-C

Variant summary

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

The NM_147164.3(CNTFR):​c.*173C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 701,960 control chromosomes in the GnomAD database, including 7,464 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 0.14 (1491 hom., cov: 32)
  • Exomes 𝑓: 0.14 (5973 hom.)
• Consequence: CNTFR NM_147164.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.295
• Publications: 13 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNTFR	NM_147164.3	c.*173C>T		3_prime_UTR_variant	Exon 10 of 10	ENST00000378980.8	NP_671693.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNTFR	ENST00000378980.8	c.*173C>T		3_prime_UTR_variant	Exon 10 of 10	1	NM_147164.3	ENSP00000368265.3
CNTFR	ENST00000351266.8	c.*173C>T		3_prime_UTR_variant	Exon 9 of 9	1		ENSP00000242338.4
CNTFR	ENST00000610543.4	c.*173C>T		3_prime_UTR_variant	Exon 10 of 10	5		ENSP00000480451.1

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20555 AN: 151990 Hom.: 1494 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.0732

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.126

GnomAD4 exome AF: 0.136 AC: 75009 AN: 549852 Hom.: 5973 Cov.: 3 AF XY: 0.138 AC XY: 41013 AN XY: 297194

African (AFR) AF: 0.148 AC: 2302 AN: 15588

American (AMR) AF: 0.184 AC: 6217 AN: 33822

Ashkenazi Jewish (ASJ) AF: 0.0771 AC: 1502 AN: 19476

East Asian (EAS) AF: 0.302 AC: 9689 AN: 32068

South Asian (SAS) AF: 0.183 AC: 11170 AN: 61074

European-Finnish (FIN) AF: 0.123 AC: 5039 AN: 40938

Middle Eastern (MID) AF: 0.123 AC: 298 AN: 2422

European-Non Finnish (NFE) AF: 0.111 AC: 34874 AN: 314316

Other (OTH) AF: 0.130 AC: 3918 AN: 30148

GnomAD4 genome AF: 0.135 AC: 20547 AN: 152108 Hom.: 1491 Cov.: 32 AF XY: 0.138 AC XY: 10271 AN XY: 74372

African (AFR) AF: 0.142 AC: 5909 AN: 41522

American (AMR) AF: 0.149 AC: 2277 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0732 AC: 254 AN: 3470

East Asian (EAS) AF: 0.300 AC: 1545 AN: 5146

South Asian (SAS) AF: 0.204 AC: 982 AN: 4822

European-Finnish (FIN) AF: 0.126 AC: 1334 AN: 10600

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.113 AC: 7706 AN: 67940

Other (OTH) AF: 0.127 AC: 267 AN: 2108

Alfa AF: 0.0956 Hom.: 276

Bravo AF: 0.137

Asia WGS AF: 0.238 AC: 824 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	9.0
DANN	Benign	0.65
PhyloP100		0.29

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs41274853; hg19: chr9-34551896; COSMIC: COSV63634023; COSMIC: COSV63634023;