17-6812865-T-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_053285.2(TEKT1):c.818A>G(p.Asp273Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00178 in 1,614,092 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_053285.2 missense
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 |
---|---|---|---|---|---|---|---|
TEKT1 | NM_053285.2 | c.818A>G | p.Asp273Gly | missense_variant | 6/8 | ENST00000338694.7 | |
TEKT1 | XM_011524027.4 | c.818A>G | p.Asp273Gly | missense_variant | 6/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TEKT1 | ENST00000338694.7 | c.818A>G | p.Asp273Gly | missense_variant | 6/8 | 1 | NM_053285.2 | P1 | |
TEKT1 | ENST00000572291.1 | c.206A>G | p.Asp69Gly | missense_variant | 2/3 | 5 | |||
TEKT1 | ENST00000571744.1 | c.152A>G | p.Asp51Gly | missense_variant | 1/2 | 3 | |||
TEKT1 | ENST00000575592.1 | c.*409A>G | 3_prime_UTR_variant, NMD_transcript_variant | 5/7 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00115 AC: 175AN: 152240Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00126 AC: 317AN: 251304Hom.: 1 AF XY: 0.00120 AC XY: 163AN XY: 135812
GnomAD4 exome AF: 0.00185 AC: 2698AN: 1461734Hom.: 4 Cov.: 31 AF XY: 0.00173 AC XY: 1257AN XY: 727154
GnomAD4 genome ? AF: 0.00115 AC: 175AN: 152358Hom.: 0 Cov.: 33 AF XY: 0.00105 AC XY: 78AN XY: 74502
ClinVar
Submissions by phenotype
TEKT1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 02, 2022 | 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