rs3751353
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP3BA1
The NM_178540.5(C1QTNF9):āc.230G>Cā(p.Gly77Ala) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00252 in 1,585,650 control chromosomes in the GnomAD database, including 138 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_178540.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
C1QTNF9 | NM_178540.5 | c.230G>C | p.Gly77Ala | missense_variant, splice_region_variant | 4/4 | ENST00000332018.5 | |
C1QTNF9 | NM_001303137.2 | c.230G>C | p.Gly77Ala | missense_variant, splice_region_variant | 5/5 | ||
C1QTNF9 | NM_001303138.2 | c.230G>C | p.Gly77Ala | missense_variant, splice_region_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C1QTNF9 | ENST00000332018.5 | c.230G>C | p.Gly77Ala | missense_variant, splice_region_variant | 4/4 | 1 | NM_178540.5 | P1 | |
C1QTNF9-AS1 | ENST00000449656.1 | n.73+530C>G | intron_variant, non_coding_transcript_variant | 5 | |||||
C1QTNF9 | ENST00000382071.6 | c.230G>C | p.Gly77Ala | missense_variant, splice_region_variant | 4/4 | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00277 AC: 412AN: 148968Hom.: 11 Cov.: 23
GnomAD3 exomes AF: 0.00915 AC: 2104AN: 229946Hom.: 72 AF XY: 0.00710 AC XY: 887AN XY: 125016
GnomAD4 exome AF: 0.00249 AC: 3581AN: 1436572Hom.: 127 Cov.: 30 AF XY: 0.00217 AC XY: 1552AN XY: 714418
GnomAD4 genome ? AF: 0.00277 AC: 413AN: 149078Hom.: 11 Cov.: 23 AF XY: 0.00291 AC XY: 211AN XY: 72496
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at