17-15327993-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_031898.3(TEKT3):c.662C>T(p.Thr221Met) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000244 in 1,613,208 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/23 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_031898.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TEKT3 | NM_031898.3 | c.662C>T | p.Thr221Met | missense_variant, splice_region_variant | 4/9 | ENST00000395930.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TEKT3 | ENST00000395930.6 | c.662C>T | p.Thr221Met | missense_variant, splice_region_variant | 4/9 | 1 | NM_031898.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000184 AC: 28AN: 152012Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000179 AC: 45AN: 251382Hom.: 0 AF XY: 0.000177 AC XY: 24AN XY: 135858
GnomAD4 exome AF: 0.000251 AC: 366AN: 1461078Hom.: 2 Cov.: 30 AF XY: 0.000250 AC XY: 182AN XY: 726924
GnomAD4 genome AF: 0.000184 AC: 28AN: 152130Hom.: 0 Cov.: 33 AF XY: 0.000175 AC XY: 13AN XY: 74380
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 16, 2021 | The c.662C>T (p.T221M) alteration is located in exon 4 (coding exon 2) of the TEKT3 gene. This alteration results from a C to T substitution at nucleotide position 662, causing the threonine (T) at amino acid position 221 to be replaced by a methionine (M). 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