1-28571871-A-T
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The ENST00000373830.4(TRNAU1AP):c.698A>T(p.Tyr233Phe) variant causes a missense change. The variant allele was found at a frequency of 0.000257 in 1,613,400 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 Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00013 ( 0 hom., cov: 30)
Exomes 𝑓: 0.00027 ( 0 hom. )
Consequence
TRNAU1AP
ENST00000373830.4 missense
ENST00000373830.4 missense
Scores
1
4
14
Clinical Significance
Conservation
PhyloP100: 6.15
Genes affected
TRNAU1AP (HGNC:30813): (tRNA selenocysteine 1 associated protein 1) Enables RNA binding activity. Predicted to be involved in selenocysteine incorporation. Predicted to be located in cytoplasm. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.10880789).
BS2
High AC in GnomAd4 at 19 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRNAU1AP | NM_017846.5 | c.698A>T | p.Tyr233Phe | missense_variant | 8/9 | ENST00000373830.4 | NP_060316.1 | |
TRNAU1AP | NR_003109.2 | n.872A>T | non_coding_transcript_exon_variant | 9/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TRNAU1AP | ENST00000373830.4 | c.698A>T | p.Tyr233Phe | missense_variant | 8/9 | 1 | NM_017846.5 | ENSP00000362936 | P1 | |
TRNAU1AP | ENST00000480930.5 | n.858A>T | non_coding_transcript_exon_variant | 9/10 | 1 | |||||
TRNAU1AP | ENST00000484775.1 | n.573A>T | non_coding_transcript_exon_variant | 6/8 | 5 | |||||
TRNAU1AP | ENST00000491577.5 | n.1316A>T | non_coding_transcript_exon_variant | 7/8 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 151834Hom.: 0 Cov.: 30
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GnomAD3 exomes AF: 0.0000477 AC: 12AN: 251472Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135908
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GnomAD4 exome AF: 0.000270 AC: 395AN: 1461448Hom.: 0 Cov.: 30 AF XY: 0.000261 AC XY: 190AN XY: 727060
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GnomAD4 genome AF: 0.000125 AC: 19AN: 151952Hom.: 0 Cov.: 30 AF XY: 0.000121 AC XY: 9AN XY: 74264
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 30, 2023 | The c.698A>T (p.Y233F) alteration is located in exon 8 (coding exon 8) of the TRNAU1AP gene. This alteration results from a A to T substitution at nucleotide position 698, causing the tyrosine (Y) at amino acid position 233 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
P
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at