rs9813489
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_145262.4(GLYCTK):c.1181C>T(p.Thr394Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0018 in 1,608,714 control chromosomes in the GnomAD database, including 39 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_145262.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GLYCTK | NM_145262.4 | c.1181C>T | p.Thr394Ile | missense_variant | 5/5 | ENST00000436784.7 | NP_660305.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GLYCTK | ENST00000436784.7 | c.1181C>T | p.Thr394Ile | missense_variant | 5/5 | 1 | NM_145262.4 | ENSP00000389175.2 |
Frequencies
GnomAD3 genomes AF: 0.00904 AC: 1376AN: 152228Hom.: 20 Cov.: 33
GnomAD3 exomes AF: 0.00250 AC: 620AN: 248344Hom.: 4 AF XY: 0.00188 AC XY: 253AN XY: 134332
GnomAD4 exome AF: 0.00104 AC: 1515AN: 1456368Hom.: 19 Cov.: 32 AF XY: 0.000881 AC XY: 638AN XY: 723800
GnomAD4 genome AF: 0.00904 AC: 1377AN: 152346Hom.: 20 Cov.: 33 AF XY: 0.00885 AC XY: 659AN XY: 74486
ClinVar
Submissions by phenotype
not provided Benign:3
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Jun 16, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 24, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at