chr1-31662337-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001856.4(COL16A1):āc.3678G>Cā(p.Leu1226Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000745 in 1,610,828 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001856.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL16A1 | NM_001856.4 | c.3678G>C | p.Leu1226Phe | missense_variant | 58/71 | ENST00000373672.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL16A1 | ENST00000373672.8 | c.3678G>C | p.Leu1226Phe | missense_variant | 58/71 | 5 | NM_001856.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151932Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.00000685 AC: 10AN: 1458896Hom.: 0 Cov.: 81 AF XY: 0.00000689 AC XY: 5AN XY: 725388
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151932Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74186
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 20, 2023 | The c.3678G>C (p.L1226F) alteration is located in exon 58 (coding exon 57) of the COL16A1 gene. This alteration results from a G to C substitution at nucleotide position 3678, causing the leucine (L) at amino acid position 1226 to be replaced by a phenylalanine (F). 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