5-34042933-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_181435.6(C1QTNF3):āc.193A>Cā(p.Thr65Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000805 in 1,613,974 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_181435.6 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
C1QTNF3 | NM_181435.6 | c.193A>C | p.Thr65Pro | missense_variant | 1/6 | ENST00000382065.8 | |
C1QTNF3-AMACR | NR_037951.1 | n.112-7175A>C | intron_variant, non_coding_transcript_variant | ||||
C1QTNF3 | NM_030945.4 | c.84+109A>C | intron_variant | ||||
C1QTNF3 | NR_146599.1 | n.895-7175A>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C1QTNF3 | ENST00000382065.8 | c.193A>C | p.Thr65Pro | missense_variant | 1/6 | 1 | NM_181435.6 | P4 | |
C1QTNF3 | ENST00000231338.7 | c.84+109A>C | intron_variant | 1 | A1 | ||||
C1QTNF3 | ENST00000508434.1 | n.171+109A>C | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152084Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251108Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135686
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461890Hom.: 0 Cov.: 31 AF XY: 0.00000688 AC XY: 5AN XY: 727246
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152084Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74284
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 03, 2022 | The c.193A>C (p.T65P) alteration is located in exon 1 (coding exon 1) of the C1QTNF3 gene. This alteration results from a A to C substitution at nucleotide position 193, causing the threonine (T) at amino acid position 65 to be replaced by a proline (P). 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