chr5-150012282-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_014983.3(HMGXB3):c.838C>T(p.Pro280Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00927 in 1,552,110 control chromosomes in the GnomAD database, including 98 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0069 ( 6 hom., cov: 32)
Exomes 𝑓: 0.0095 ( 92 hom. )
Consequence
HMGXB3
NM_014983.3 missense
NM_014983.3 missense
Scores
1
4
11
Clinical Significance
Conservation
PhyloP100: 3.79
Genes affected
HMGXB3 (HGNC:28982): (HMG-box containing 3) This gene is one of the non-canonical high mobility group (HMG) genes. The encoded protein contains an HMG-box domain found in DNA binding proteins such as transcription factors and chromosomal proteins. [provided by RefSeq, Aug 2011]
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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=0.0049375296).
BP6
?
Variant 5-150012282-C-T is Benign according to our data. Variant chr5-150012282-C-T is described in ClinVar as [Benign]. Clinvar id is 773464.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAd at 6 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HMGXB3 | NM_014983.3 | c.838C>T | p.Pro280Ser | missense_variant | 5/20 | ENST00000502717.6 | |
HMGXB3 | NM_001366501.2 | c.340C>T | p.Pro114Ser | missense_variant | 4/19 | ||
HMGXB3 | XM_047416963.1 | c.838C>T | p.Pro280Ser | missense_variant | 5/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HMGXB3 | ENST00000502717.6 | c.838C>T | p.Pro280Ser | missense_variant | 5/20 | 1 | NM_014983.3 | P2 | |
HMGXB3 | ENST00000613459.4 | c.1576C>T | p.Pro526Ser | missense_variant | 6/21 | 5 | A2 | ||
HMGXB3 | ENST00000503427.5 | c.838C>T | p.Pro280Ser | missense_variant | 5/21 | 5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00690 AC: 1050AN: 152178Hom.: 6 Cov.: 32
GnomAD3 genomes
?
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1050
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152178
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GnomAD3 exomes AF: 0.00588 AC: 935AN: 158950Hom.: 8 AF XY: 0.00552 AC XY: 462AN XY: 83706
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GnomAD4 exome AF: 0.00953 AC: 13344AN: 1399814Hom.: 92 Cov.: 30 AF XY: 0.00915 AC XY: 6315AN XY: 690414
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GnomAD4 genome ? AF: 0.00689 AC: 1050AN: 152296Hom.: 6 Cov.: 32 AF XY: 0.00681 AC XY: 507AN XY: 74482
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TwinsUK
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52
ESP6500AA
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ESP6500EA
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ExAC
?
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89
Asia WGS
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AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 27, 2017 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
Cadd
Benign
Dann
Uncertain
DEOGEN2
Benign
T;T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T;T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;.;.
MutationTaster
Benign
D;D
PrimateAI
Benign
T
Sift4G
Benign
T;D;D
Polyphen
B;.;.
Vest4
MVP
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