13-24316146-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_178540.5(C1QTNF9):c.143C>T(p.Ala48Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000952 in 1,606,720 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/20 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
C1QTNF9 | NM_178540.5 | c.143C>T | p.Ala48Val | missense_variant | Exon 2 of 4 | ENST00000332018.5 | NP_848635.2 | |
C1QTNF9 | NM_001303137.2 | c.143C>T | p.Ala48Val | missense_variant | Exon 3 of 5 | NP_001290066.1 | ||
C1QTNF9 | NM_001303138.2 | c.143C>T | p.Ala48Val | missense_variant | Exon 2 of 4 | NP_001290067.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
C1QTNF9 | ENST00000332018.5 | c.143C>T | p.Ala48Val | missense_variant | Exon 2 of 4 | 1 | NM_178540.5 | ENSP00000333737.4 | ||
ENSG00000273167 | ENST00000382141.4 | n.*139C>T | non_coding_transcript_exon_variant | Exon 14 of 16 | 5 | ENSP00000371576.4 | ||||
ENSG00000273167 | ENST00000382141.4 | n.*139C>T | 3_prime_UTR_variant | Exon 14 of 16 | 5 | ENSP00000371576.4 |
Frequencies
GnomAD3 genomes AF: 0.0000796 AC: 12AN: 150686Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.000137 AC: 34AN: 248144Hom.: 0 AF XY: 0.000127 AC XY: 17AN XY: 134108
GnomAD4 exome AF: 0.0000968 AC: 141AN: 1456034Hom.: 0 Cov.: 33 AF XY: 0.000105 AC XY: 76AN XY: 723576
GnomAD4 genome AF: 0.0000796 AC: 12AN: 150686Hom.: 0 Cov.: 30 AF XY: 0.0000953 AC XY: 7AN XY: 73466
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.143C>T (p.A48V) alteration is located in exon 2 (coding exon 1) of the C1QTNF9 gene. This alteration results from a C to T substitution at nucleotide position 143, causing the alanine (A) at amino acid position 48 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