X-129911838-C-T
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_006649.4(UTP14A):c.454C>T(p.Arg152Trp) variant causes a missense change. The variant allele was found at a frequency of 0.0000107 in 1,209,388 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000090 ( 0 hom., 0 hem., cov: 22)
Exomes 𝑓: 0.000011 ( 0 hom. 4 hem. )
Consequence
UTP14A
NM_006649.4 missense
NM_006649.4 missense
Scores
3
7
7
Clinical Significance
Conservation
PhyloP100: 4.33
Genes affected
UTP14A (HGNC:10665): (UTP14A small subunit processome component) This gene encodes a member of the uridine triphosphate 14 family. As an essential component of a large ribonucleoprotein complex bound to the U3 small nucleolar RNA, the encoded protein is involved in ribosome biogenesis and 18S rRNA synthesis. An autosomal retrotransposed copy of this X-linked gene exists on chromosome 13. Alternative splicing results in multiple transcript variants.[provided by RefSeq, Oct 2009]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BS2
High Hemizygotes in GnomAdExome4 at 4 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
UTP14A | NM_006649.4 | c.454C>T | p.Arg152Trp | missense_variant | 6/15 | ENST00000394422.8 | NP_006640.2 | |
UTP14A | NM_001166221.2 | c.381+688C>T | intron_variant | NP_001159693.1 | ||||
LOC105373335 | NR_188631.1 | n.219-3285G>A | intron_variant |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000899 AC: 1AN: 111274Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33460
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GnomAD3 exomes AF: 0.0000491 AC: 9AN: 183389Hom.: 0 AF XY: 0.0000442 AC XY: 3AN XY: 67835
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GnomAD4 exome AF: 0.0000109 AC: 12AN: 1098114Hom.: 0 Cov.: 30 AF XY: 0.0000110 AC XY: 4AN XY: 363476
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GnomAD4 genome AF: 0.00000899 AC: 1AN: 111274Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33460
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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 | Sep 11, 2024 | The c.454C>T (p.R152W) alteration is located in exon 6 (coding exon 6) of the UTP14A gene. This alteration results from a C to T substitution at nucleotide position 454, causing the arginine (R) at amino acid position 152 to be replaced by a tryptophan (W). 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
Uncertain
DEOGEN2
Benign
T
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D
M_CAP
Uncertain
D
MetaRNN
Uncertain
D
MetaSVM
Benign
T
MutationAssessor
Pathogenic
H
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D
REVEL
Uncertain
Sift
Benign
D
Sift4G
Uncertain
D
Polyphen
B
Vest4
MutPred
Gain of ubiquitination at K150 (P = 0.0716);
MVP
MPC
ClinPred
D
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