chr20-62840721-C-A
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_001853.4(COL9A3):c.2044C>A(p.Arg682=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0894 in 1,571,590 control chromosomes in the GnomAD database, including 9,005 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. R682R) has been classified as Likely benign.
Frequency
Consequence
NM_001853.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL9A3 | NM_001853.4 | c.2044C>A | p.Arg682= | synonymous_variant | 32/32 | ENST00000649368.1 | |
COL9A3 | XM_047439893.1 | c.2221C>A | p.Arg741= | synonymous_variant | 31/31 | ||
COL9A3 | XM_047439894.1 | c.1483C>A | p.Arg495= | synonymous_variant | 32/32 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL9A3 | ENST00000649368.1 | c.2044C>A | p.Arg682= | synonymous_variant | 32/32 | NM_001853.4 | P1 | ||
COL9A3 | ENST00000467819.5 | n.555C>A | non_coding_transcript_exon_variant | 4/4 | 1 | ||||
COL9A3 | ENST00000462700.5 | n.799C>A | non_coding_transcript_exon_variant | 6/6 | 3 | ||||
COL9A3 | ENST00000466192.5 | n.1771C>A | non_coding_transcript_exon_variant | 8/8 | 2 |
Frequencies
GnomAD3 genomes AF: 0.149 AC: 22664AN: 151974Hom.: 2521 Cov.: 32
GnomAD3 exomes AF: 0.0975 AC: 17463AN: 179196Hom.: 1230 AF XY: 0.0938 AC XY: 8951AN XY: 95426
GnomAD4 exome AF: 0.0830 AC: 117838AN: 1419498Hom.: 6481 Cov.: 32 AF XY: 0.0828 AC XY: 58101AN XY: 702042
GnomAD4 genome AF: 0.149 AC: 22701AN: 152092Hom.: 2524 Cov.: 32 AF XY: 0.145 AC XY: 10775AN XY: 74338
ClinVar
Submissions by phenotype
not specified Benign:5
Benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, Amsterdam University Medical Center | - | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 15, 2017 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at