rs9469081
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001365276.2(TNXB):c.6379G>A(p.Val2127Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 1,613,126 control chromosomes in the GnomAD database, including 15,033 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V2127G) has been classified as Uncertain significance.
Frequency
Consequence
NM_001365276.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNXB | NM_001365276.2 | c.6379G>A | p.Val2127Met | missense_variant | 18/44 | ENST00000644971.2 | |
TNXB | NM_019105.8 | c.6379G>A | p.Val2127Met | missense_variant | 18/44 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNXB | ENST00000644971.2 | c.6379G>A | p.Val2127Met | missense_variant | 18/44 | NM_001365276.2 | |||
TNXB | ENST00000647633.1 | c.7120G>A | p.Val2374Met | missense_variant | 19/45 | P1 | |||
TNXB | ENST00000375244.7 | c.6379G>A | p.Val2127Met | missense_variant | 18/44 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.149 AC: 22573AN: 152004Hom.: 2183 Cov.: 32
GnomAD3 exomes AF: 0.139 AC: 34607AN: 248520Hom.: 3581 AF XY: 0.151 AC XY: 20344AN XY: 134924
GnomAD4 exome AF: 0.111 AC: 162430AN: 1461004Hom.: 12839 Cov.: 32 AF XY: 0.119 AC XY: 86359AN XY: 726804
GnomAD4 genome ? AF: 0.149 AC: 22607AN: 152122Hom.: 2194 Cov.: 32 AF XY: 0.152 AC XY: 11290AN XY: 74380
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 09, 2018 | - - |
Cardiovascular phenotype Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 31, 2018 | This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at