chr1-31662642-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001856.4(COL16A1):c.3572G>A(p.Arg1191Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000122 in 1,398,508 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001856.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL16A1 | NM_001856.4 | c.3572G>A | p.Arg1191Gln | missense_variant | 57/71 | ENST00000373672.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL16A1 | ENST00000373672.8 | c.3572G>A | p.Arg1191Gln | missense_variant | 57/71 | 5 | NM_001856.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 1AN: 151530Hom.: 0 Cov.: 31 FAILED QC
GnomAD3 exomes AF: 0.0000327 AC: 5AN: 152852Hom.: 0 AF XY: 0.0000368 AC XY: 3AN XY: 81582
GnomAD4 exome AF: 0.0000122 AC: 17AN: 1398508Hom.: 0 Cov.: 36 AF XY: 0.0000145 AC XY: 10AN XY: 689972
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000659 AC: 1AN: 151642Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74088
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 17, 2021 | The c.3572G>A (p.R1191Q) alteration is located in exon 57 (coding exon 56) of the COL16A1 gene. This alteration results from a G to A substitution at nucleotide position 3572, causing the arginine (R) at amino acid position 1191 to be replaced by a glutamine (Q). 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