chr13-24321757-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_178540.5(C1QTNF9):c.991A>G(p.Ser331Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000038 in 1,577,876 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_178540.5 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
C1QTNF9 | NM_178540.5 | c.991A>G | p.Ser331Gly | missense_variant | 4/4 | ENST00000332018.5 | |
C1QTNF9 | NM_001303137.2 | c.991A>G | p.Ser331Gly | missense_variant | 5/5 | ||
C1QTNF9 | NM_001303138.2 | c.991A>G | p.Ser331Gly | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C1QTNF9 | ENST00000332018.5 | c.991A>G | p.Ser331Gly | missense_variant | 4/4 | 1 | NM_178540.5 | P1 | |
C1QTNF9 | ENST00000382071.6 | c.991A>G | p.Ser331Gly | missense_variant | 4/4 | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152224Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.00000439 AC: 1AN: 227554Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 121906
GnomAD4 exome AF: 0.00000351 AC: 5AN: 1425652Hom.: 0 Cov.: 33 AF XY: 0.00000142 AC XY: 1AN XY: 703786
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152224Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 74364
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 11, 2022 | The c.991A>G (p.S331G) alteration is located in exon 4 (coding exon 3) of the C1QTNF9 gene. This alteration results from a A to G substitution at nucleotide position 991, causing the serine (S) at amino acid position 331 to be replaced by a glycine (G). 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