chr1-31658916-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001856.4(COL16A1):c.3928G>T(p.Val1310Leu) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 17/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001856.4 missense, splice_region
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.3928G>T | p.Val1310Leu | missense_variant, splice_region_variant | 63/71 | ENST00000373672.8 | |
PEF1-AS1 | NR_184311.1 | n.836-738C>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL16A1 | ENST00000373672.8 | c.3928G>T | p.Val1310Leu | missense_variant, splice_region_variant | 63/71 | 5 | NM_001856.4 | P1 | |
PEF1-AS1 | ENST00000609549.5 | n.623-782C>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1401328Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 691318
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 02, 2024 | The c.3928G>T (p.V1310L) alteration is located in exon 63 (coding exon 62) of the COL16A1 gene. This alteration results from a G to T substitution at nucleotide position 3928, causing the valine (V) at amino acid position 1310 to be replaced by a leucine (L). 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
Publications
No publications associated with this variant yet.