chr6-31972121-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_005510.4(DXO):c.-199G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0037 in 1,613,054 control chromosomes in the GnomAD database, including 22 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0037 ( 1 hom., cov: 32)
Exomes 𝑓: 0.0037 ( 21 hom. )
Consequence
DXO
NM_005510.4 5_prime_UTR
NM_005510.4 5_prime_UTR
Scores
1
1
14
Clinical Significance
Conservation
PhyloP100: -0.0310
Genes affected
DXO (HGNC:2992): (decapping exoribonuclease) This gene localizes to the major histocompatibility complex (MHC) class III region on chromosome 6. The function of its protein product is unknown, but its ubiquitous expression and conservation in both simple and complex eukaryotes suggests that this may be a housekeeping gene. [provided by RefSeq, Jul 2008]
STK19 (HGNC:11398): (serine/threonine kinase 19) This gene encodes a serine/threonine kinase which localizes predominantly to the nucleus. Its specific function is unknown; it is possible that phosphorylation of this protein is involved in transcriptional regulation. This gene localizes to the major histocompatibility complex (MHC) class III region on chromosome 6 and expresses two transcript variants. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.004273206).
BP6
?
Variant 6-31972121-C-T is Benign according to our data. Variant chr6-31972121-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2656433.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAdExome at 4 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DXO | NM_005510.4 | c.-199G>A | 5_prime_UTR_variant | 1/7 | ENST00000337523.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DXO | ENST00000337523.10 | c.-199G>A | 5_prime_UTR_variant | 1/7 | 1 | NM_005510.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00369 AC: 561AN: 152230Hom.: 1 Cov.: 32
GnomAD3 genomes
?
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561
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GnomAD3 exomes AF: 0.00377 AC: 930AN: 246570Hom.: 4 AF XY: 0.00382 AC XY: 513AN XY: 134266
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GnomAD4 exome AF: 0.00370 AC: 5407AN: 1460708Hom.: 21 Cov.: 31 AF XY: 0.00370 AC XY: 2686AN XY: 726630
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GnomAD4 genome ? AF: 0.00368 AC: 561AN: 152346Hom.: 1 Cov.: 32 AF XY: 0.00380 AC XY: 283AN XY: 74494
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2023 | STK19: BP4, BS2 - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;.;.
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
N;N;N;N
PrimateAI
Benign
T
PROVEAN
Uncertain
D;N;N
REVEL
Benign
Sift
Pathogenic
D;D;D
Sift4G
Benign
T;T;T
Polyphen
0.0010
.;B;B
Vest4
0.12, 0.10
MVP
MPC
0.53
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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