chr17-7845894-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001348716.2(KDM6B):c.160C>T(p.Pro54Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000161 in 1,613,710 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 (★).
Frequency
Consequence
NM_001348716.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KDM6B | NM_001348716.2 | c.160C>T | p.Pro54Ser | missense_variant | 6/24 | ENST00000448097.7 | |
KDM6B | NM_001080424.2 | c.160C>T | p.Pro54Ser | missense_variant | 5/22 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KDM6B | ENST00000448097.7 | c.160C>T | p.Pro54Ser | missense_variant | 6/24 | 5 | NM_001348716.2 | A2 | |
KDM6B | ENST00000254846.9 | c.160C>T | p.Pro54Ser | missense_variant | 5/22 | 1 | P2 | ||
KDM6B | ENST00000570632.1 | c.160C>T | p.Pro54Ser | missense_variant | 4/9 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152230Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251406Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135872
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1461362Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 10AN XY: 727006
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152348Hom.: 0 Cov.: 33 AF XY: 0.0000268 AC XY: 2AN XY: 74504
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 03, 2022 | The c.160C>T (p.P54S) alteration is located in exon 5 (coding exon 2) of the KDM6B gene. This alteration results from a C to T substitution at nucleotide position 160, causing the proline (P) at amino acid position 54 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