chr6-69936899-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001858.6(COL19A1):c.862A>G(p.Ile288Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000248 in 1,612,790 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001858.6 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 |
---|---|---|---|---|---|---|---|
COL19A1 | NM_001858.6 | c.862A>G | p.Ile288Val | missense_variant | 8/51 | ENST00000620364.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL19A1 | ENST00000620364.5 | c.862A>G | p.Ile288Val | missense_variant | 8/51 | 1 | NM_001858.6 | P1 | |
COL19A1 | ENST00000483745.1 | n.28A>G | non_coding_transcript_exon_variant | 1/5 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 250142Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135180
GnomAD4 exome AF: 0.0000260 AC: 38AN: 1460602Hom.: 0 Cov.: 30 AF XY: 0.0000151 AC XY: 11AN XY: 726608
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152188Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 27, 2022 | The c.862A>G (p.I288V) alteration is located in exon 8 (coding exon 7) of the COL19A1 gene. This alteration results from a A to G substitution at nucleotide position 862, causing the isoleucine (I) at amino acid position 288 to be replaced by a valine (V). 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