NM_001365276.2:c.10723T>C
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBP6_Very_Strong
The NM_001365276.2(TNXB):c.10723T>C(p.Ser3575Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 1,553,184 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 Benign (★★).
Frequency
Consequence
NM_001365276.2 missense
Scores
Clinical Significance
Conservation
Publications
- Ehlers-Danlos syndromeInheritance: AR Classification: DEFINITIVE Submitted by: G2P
- Ehlers-Danlos syndrome due to tenascin-X deficiencyInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Genomics England PanelApp, Illumina, PanelApp Australia, Orphanet
- familial vesicoureteral refluxInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- vesicoureteral reflux 8Inheritance: AD Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)
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ACMG classification
Our verdict: Benign. The variant received -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TNXB | NM_001365276.2 | c.10723T>C | p.Ser3575Pro | missense_variant | Exon 32 of 44 | ENST00000644971.2 | NP_001352205.1 | |
TNXB | NM_001428335.1 | c.11464T>C | p.Ser3822Pro | missense_variant | Exon 33 of 45 | NP_001415264.1 | ||
TNXB | NM_019105.8 | c.10717T>C | p.Ser3573Pro | missense_variant | Exon 32 of 44 | NP_061978.6 | ||
TNXB | NM_032470.4 | c.10T>C | p.Ser4Pro | missense_variant | Exon 1 of 13 | NP_115859.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.149 AC: 21454AN: 144376Hom.: 0 Cov.: 24 show subpopulations
GnomAD2 exomes AF: 0.114 AC: 26206AN: 230376 AF XY: 0.117 show subpopulations
GnomAD4 exome AF: 0.118 AC: 166189AN: 1408718Hom.: 1 Cov.: 33 AF XY: 0.119 AC XY: 83568AN XY: 700502 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
Age Distribution
GnomAD4 genome AF: 0.149 AC: 21472AN: 144466Hom.: 0 Cov.: 24 AF XY: 0.147 AC XY: 10338AN XY: 70560 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
Age Distribution
ClinVar
Submissions by phenotype
not specified Benign:1
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at