chr3-177026467-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 3P and 9B. PM1PP2BP4_StrongBP6BS2
The NM_024665.7(TBL1XR1):c.1424C>T(p.Ala475Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000376 in 1,595,132 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. A475A) has been classified as Likely benign.
Frequency
Consequence
NM_024665.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TBL1XR1 | NM_024665.7 | c.1424C>T | p.Ala475Val | missense_variant | 15/16 | ENST00000457928.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBL1XR1 | ENST00000457928.7 | c.1424C>T | p.Ala475Val | missense_variant | 15/16 | 1 | NM_024665.7 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152052Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000205 AC: 47AN: 228730Hom.: 0 AF XY: 0.000120 AC XY: 15AN XY: 124704
GnomAD4 exome AF: 0.0000367 AC: 53AN: 1443080Hom.: 0 Cov.: 30 AF XY: 0.0000237 AC XY: 17AN XY: 717862
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152052Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74272
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Aug 01, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 30, 2020 | - - |
Inborn genetic diseases Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 31, 2020 | 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. - |
Pierpont syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 09, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at