1-36085859-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_014466.3(TEKT2):c.306C>G(p.Asn102Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000088 in 1,613,844 control chromosomes in the GnomAD database, including 1 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 Uncertain significance (★).
Frequency
Consequence
NM_014466.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TEKT2 | NM_014466.3 | c.306C>G | p.Asn102Lys | missense_variant | 4/10 | ENST00000207457.8 | |
TEKT2 | XM_005270753.3 | c.306C>G | p.Asn102Lys | missense_variant | 4/10 | ||
TEKT2 | XM_011541258.4 | c.306C>G | p.Asn102Lys | missense_variant | 4/10 | ||
TEKT2 | XM_017001055.2 | c.306C>G | p.Asn102Lys | missense_variant | 4/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TEKT2 | ENST00000207457.8 | c.306C>G | p.Asn102Lys | missense_variant | 4/10 | 1 | NM_014466.3 | P1 | |
TEKT2 | ENST00000469024.1 | c.*110C>G | 3_prime_UTR_variant, NMD_transcript_variant | 4/10 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000105 AC: 16AN: 152140Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000160 AC: 40AN: 249802Hom.: 0 AF XY: 0.000214 AC XY: 29AN XY: 135382
GnomAD4 exome AF: 0.0000862 AC: 126AN: 1461586Hom.: 1 Cov.: 31 AF XY: 0.000117 AC XY: 85AN XY: 727076
GnomAD4 genome ? AF: 0.000105 AC: 16AN: 152258Hom.: 0 Cov.: 31 AF XY: 0.000148 AC XY: 11AN XY: 74458
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 31, 2023 | The c.306C>G (p.N102K) alteration is located in exon 4 (coding exon 3) of the TEKT2 gene. This alteration results from a C to G substitution at nucleotide position 306, causing the asparagine (N) at amino acid position 102 to be replaced by a lysine (K). 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