chr16-10676107-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_144674.2(TEKT5):c.938C>G(p.Ser313Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000502 in 1,614,208 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00024 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000031 ( 1 hom. )
Consequence
TEKT5
NM_144674.2 missense
NM_144674.2 missense
Scores
7
12
Clinical Significance
Conservation
PhyloP100: 5.07
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.097385526).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TEKT5 | NM_144674.2 | c.938C>G | p.Ser313Cys | missense_variant | 5/7 | ENST00000283025.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TEKT5 | ENST00000283025.7 | c.938C>G | p.Ser313Cys | missense_variant | 5/7 | 1 | NM_144674.2 | P1 | |
TEKT5 | ENST00000576638.1 | c.257C>G | p.Ser86Cys | missense_variant | 4/5 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000230 AC: 35AN: 152200Hom.: 0 Cov.: 33
GnomAD3 genomes
?
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GnomAD3 exomes AF: 0.0000517 AC: 13AN: 251386Hom.: 0 AF XY: 0.0000662 AC XY: 9AN XY: 135850
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GnomAD4 exome AF: 0.0000308 AC: 45AN: 1461890Hom.: 1 Cov.: 36 AF XY: 0.0000344 AC XY: 25AN XY: 727248
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GnomAD4 genome ? AF: 0.000236 AC: 36AN: 152318Hom.: 0 Cov.: 33 AF XY: 0.000215 AC XY: 16AN XY: 74474
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 14, 2023 | The c.938C>G (p.S313C) alteration is located in exon 5 (coding exon 5) of the TEKT5 gene. This alteration results from a C to G substitution at nucleotide position 938, causing the serine (S) at amino acid position 313 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Uncertain
DEOGEN2
Benign
T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;.
MutationTaster
Benign
D
PrimateAI
Benign
T
PROVEAN
Uncertain
D;.
REVEL
Benign
Sift
Benign
D;.
Sift4G
Uncertain
T;.
Polyphen
P;.
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at