chr11-47590227-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_031909.3(C1QTNF4):c.584G>T(p.Gly195Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000594 in 1,532,862 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_031909.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
C1QTNF4 | NM_031909.3 | c.584G>T | p.Gly195Val | missense_variant | Exon 2 of 2 | ENST00000302514.4 | NP_114115.2 | |
C1QTNF4 | XM_017017166.2 | c.584G>T | p.Gly195Val | missense_variant | Exon 3 of 3 | XP_016872655.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000260 AC: 39AN: 150230Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000901 AC: 13AN: 144232Hom.: 0 AF XY: 0.000124 AC XY: 10AN XY: 80360
GnomAD4 exome AF: 0.0000376 AC: 52AN: 1382522Hom.: 0 Cov.: 32 AF XY: 0.0000439 AC XY: 30AN XY: 682600
GnomAD4 genome AF: 0.000259 AC: 39AN: 150340Hom.: 0 Cov.: 32 AF XY: 0.000272 AC XY: 20AN XY: 73430
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.584G>T (p.G195V) alteration is located in exon 2 (coding exon 1) of the C1QTNF4 gene. This alteration results from a G to T substitution at nucleotide position 584, causing the glycine (G) at amino acid position 195 to be replaced by a valine (V). 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