3-177047538-T-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_024665.7(TBL1XR1):c.714A>T(p.Thr238=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,612,882 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. T238T) has been classified as Likely benign.
Frequency
Consequence
NM_024665.7 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TBL1XR1 | NM_024665.7 | c.714A>T | p.Thr238= | synonymous_variant | 8/16 | ENST00000457928.7 | |
TBL1XR1-AS1 | NR_174966.1 | n.518-96T>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBL1XR1 | ENST00000457928.7 | c.714A>T | p.Thr238= | synonymous_variant | 8/16 | 1 | NM_024665.7 | P1 | |
TBL1XR1-AS1 | ENST00000617758.1 | n.530-96T>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152200Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000403 AC: 1AN: 248254Hom.: 0 AF XY: 0.00000742 AC XY: 1AN XY: 134684
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1460564Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 726552
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152318Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74498
ClinVar
Submissions by phenotype
Pierpont syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 13, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at