17-6800863-C-A
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_053285.2(TEKT1):c.933G>T(p.Lys311Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00066 in 1,614,162 control chromosomes in the GnomAD database, including 25 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_053285.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000559 AC: 85AN: 152166Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.000700 AC: 176AN: 251322Hom.: 2 AF XY: 0.000655 AC XY: 89AN XY: 135814
GnomAD4 exome AF: 0.000671 AC: 981AN: 1461878Hom.: 22 Cov.: 31 AF XY: 0.000697 AC XY: 507AN XY: 727238
GnomAD4 genome AF: 0.000558 AC: 85AN: 152284Hom.: 3 Cov.: 32 AF XY: 0.000537 AC XY: 40AN XY: 74452
ClinVar
Submissions by phenotype
TEKT1-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