13-24316068-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_178540.5(C1QTNF9):c.65C>T(p.Thr22Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000372 in 1,613,634 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T22N) has been classified as Uncertain significance.
Frequency
Consequence
NM_178540.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
C1QTNF9 | NM_178540.5 | c.65C>T | p.Thr22Ile | missense_variant | Exon 2 of 4 | ENST00000332018.5 | NP_848635.2 | |
C1QTNF9 | NM_001303137.2 | c.65C>T | p.Thr22Ile | missense_variant | Exon 3 of 5 | NP_001290066.1 | ||
C1QTNF9 | NM_001303138.2 | c.65C>T | p.Thr22Ile | 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.65C>T | p.Thr22Ile | missense_variant | Exon 2 of 4 | 1 | NM_178540.5 | ENSP00000333737.4 | ||
ENSG00000273167 | ENST00000382141.4 | n.*61C>T | non_coding_transcript_exon_variant | Exon 14 of 16 | 5 | ENSP00000371576.4 | ||||
ENSG00000273167 | ENST00000382141.4 | n.*61C>T | 3_prime_UTR_variant | Exon 14 of 16 | 5 | ENSP00000371576.4 |
Frequencies
GnomAD3 genomes AF: 0.00000659 AC: 1AN: 151850Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251408Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135870
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461784Hom.: 0 Cov.: 33 AF XY: 0.00000275 AC XY: 2AN XY: 727204
GnomAD4 genome AF: 0.00000659 AC: 1AN: 151850Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 74174
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at