Y-7070228-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_ModerateBP6BS2_Supporting
The NM_033284.2(TBL1Y):c.490G>A(p.Asp164Asn) variant causes a missense change. In-silico tool predicts a benign outcome for this variant. 11/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_033284.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TBL1Y | NM_033284.2 | c.490G>A | p.Asp164Asn | missense_variant | Exon 9 of 19 | ENST00000383032.6 | NP_150600.1 | |
TBL1Y | NM_134258.2 | c.490G>A | p.Asp164Asn | missense_variant | Exon 8 of 18 | NP_599020.1 | ||
TBL1Y | NM_134259.2 | c.490G>A | p.Asp164Asn | missense_variant | Exon 8 of 18 | NP_599021.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TBL1Y | ENST00000383032.6 | c.490G>A | p.Asp164Asn | missense_variant | Exon 9 of 19 | 1 | NM_033284.2 | ENSP00000372499.1 | ||
TBL1Y | ENST00000346432.3 | c.490G>A | p.Asp164Asn | missense_variant | Exon 8 of 18 | 1 | ENSP00000328879.4 | |||
TBL1Y | ENST00000355162.6 | c.490G>A | p.Asp164Asn | missense_variant | Exon 8 of 18 | 1 | ENSP00000347289.2 |
Frequencies
GnomAD3 genomes AF: 0.000119 AC: 4AN: 33575Hom.: 0 Cov.: 0 AF XY: 0.000119 AC XY: 4AN XY: 33575
GnomAD3 exomes AF: 0.000163 AC: 11AN: 67645Hom.: 0 AF XY: 0.000163 AC XY: 11AN XY: 67645
GnomAD4 exome AF: 0.000335 AC: 121AN: 360973Hom.: 0 Cov.: 0 AF XY: 0.000335 AC XY: 121AN XY: 360973
GnomAD4 genome AF: 0.000119 AC: 4AN: 33575Hom.: 0 Cov.: 0 AF XY: 0.000119 AC XY: 4AN XY: 33575
ClinVar
Submissions by phenotype
TBL1Y-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at