chr8-138606391-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_152888.3(COL22A1):c.4094G>A(p.Arg1365His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000527 in 1,612,878 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1365C) has been classified as Uncertain significance.
Frequency
Consequence
NM_152888.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL22A1 | NM_152888.3 | c.4094G>A | p.Arg1365His | missense_variant | 58/65 | ENST00000303045.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL22A1 | ENST00000303045.11 | c.4094G>A | p.Arg1365His | missense_variant | 58/65 | 1 | NM_152888.3 | P1 | |
COL22A1 | ENST00000341807.8 | n.1779G>A | non_coding_transcript_exon_variant | 32/39 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152152Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 247772Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134100
GnomAD4 exome AF: 0.0000534 AC: 78AN: 1460608Hom.: 0 Cov.: 31 AF XY: 0.0000592 AC XY: 43AN XY: 726478
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152270Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74452
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Clinical Genomics Laboratory, Washington University in St. Louis | Jan 29, 2024 | The COL22A1 c.4094G>A (p.Arg1365His) variant, to our knowledge, has not been reported in the medical literature and is only observed on 7/279160 alleles in the general population (gnomAD v.2.1.1), indicating it is not a common variant. Computational predictors are uncertain as to the impact of this variant on COL22A1 function. Due to limited information, the clinical significance of this variant is uncertain. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at