9-34552180-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_147164.3(CNTFR):c.1099G>A(p.Ala367Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000132 in 1,595,848 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_147164.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CNTFR | ENST00000378980.8 | c.1099G>A | p.Ala367Thr | missense_variant | Exon 9 of 10 | 1 | NM_147164.3 | ENSP00000368265.3 | ||
CNTFR | ENST00000351266.8 | c.1099G>A | p.Ala367Thr | missense_variant | Exon 8 of 9 | 1 | ENSP00000242338.4 | |||
CNTFR | ENST00000610543.4 | c.1099G>A | p.Ala367Thr | missense_variant | Exon 9 of 10 | 5 | ENSP00000480451.1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152086Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000373 AC: 8AN: 214324Hom.: 0 AF XY: 0.0000429 AC XY: 5AN XY: 116512
GnomAD4 exome AF: 0.0000132 AC: 19AN: 1443762Hom.: 0 Cov.: 32 AF XY: 0.0000126 AC XY: 9AN XY: 716348
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152086Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74286
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1099G>A (p.A367T) alteration is located in exon 9 (coding exon 7) of the CNTFR gene. This alteration results from a G to A substitution at nucleotide position 1099, causing the alanine (A) at amino acid position 367 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at