chr2-27092383-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6BP7
The NM_006488.3(KHK):c.144C>T(p.Thr48Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000322 in 1,613,678 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_006488.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KHK | ENST00000260598.10 | c.144C>T | p.Thr48Thr | synonymous_variant | Exon 2 of 8 | 2 | NM_006488.3 | ENSP00000260598.5 | ||
KHK | ENST00000260599.11 | c.144C>T | p.Thr48Thr | synonymous_variant | Exon 2 of 8 | 1 | ENSP00000260599.6 | |||
KHK | ENST00000429697.2 | c.144C>T | p.Thr48Thr | synonymous_variant | Exon 2 of 9 | 5 | ENSP00000404741.2 | |||
KHK | ENST00000490823.5 | n.492C>T | non_coding_transcript_exon_variant | Exon 4 of 10 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152224Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000598 AC: 15AN: 251016Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135778
GnomAD4 exome AF: 0.0000281 AC: 41AN: 1461336Hom.: 0 Cov.: 30 AF XY: 0.0000261 AC XY: 19AN XY: 727028
GnomAD4 genome AF: 0.0000722 AC: 11AN: 152342Hom.: 0 Cov.: 34 AF XY: 0.0000671 AC XY: 5AN XY: 74490
ClinVar
Submissions by phenotype
KHK-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at