chr16-1367751-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001372107.1(UNKL):c.1693C>T(p.Pro565Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000761 in 1,576,130 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001372107.1 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 |
---|---|---|---|---|---|---|---|
UNKL | NM_001372107.1 | c.1693C>T | p.Pro565Ser | missense_variant | 13/15 | ENST00000389221.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UNKL | ENST00000389221.9 | c.1693C>T | p.Pro565Ser | missense_variant | 13/15 | 5 | NM_001372107.1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000330 AC: 5AN: 151694Hom.: 0 Cov.: 28
GnomAD3 exomes AF: 0.0000158 AC: 3AN: 190258Hom.: 0 AF XY: 0.0000295 AC XY: 3AN XY: 101644
GnomAD4 exome AF: 0.00000491 AC: 7AN: 1424436Hom.: 0 Cov.: 37 AF XY: 0.00000426 AC XY: 3AN XY: 704716
GnomAD4 genome AF: 0.0000330 AC: 5AN: 151694Hom.: 0 Cov.: 28 AF XY: 0.0000270 AC XY: 2AN XY: 74046
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 27, 2024 | The c.1684C>T (p.P562S) alteration is located in exon 13 (coding exon 13) of the UNKL gene. This alteration results from a C to T substitution at nucleotide position 1684, causing the proline (P) at amino acid position 562 to be replaced by a serine (S). 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