chr11-47589846-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.965G>T(p.Gly322Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000304 in 1,547,044 control chromosomes in the GnomAD database, including 1 homozygotes. 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G322C) has been classified as Uncertain significance.
Frequency
Consequence
NM_031909.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
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.965G>T | p.Gly322Val | missense_variant | Exon 2 of 2 | ENST00000302514.4 | NP_114115.2 | |
C1QTNF4 | XM_017017166.2 | c.965G>T | p.Gly322Val | missense_variant | Exon 3 of 3 | XP_016872655.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000158 AC: 24AN: 152106Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000401 AC: 6AN: 149644Hom.: 0 AF XY: 0.0000377 AC XY: 3AN XY: 79478
GnomAD4 exome AF: 0.0000172 AC: 24AN: 1394822Hom.: 1 Cov.: 32 AF XY: 0.0000160 AC XY: 11AN XY: 687750
GnomAD4 genome AF: 0.000151 AC: 23AN: 152222Hom.: 0 Cov.: 33 AF XY: 0.000134 AC XY: 10AN XY: 74436
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.965G>T (p.G322V) 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 965, causing the glycine (G) at amino acid position 322 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