chrX-154545836-C-CA
Position:
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_001360016.2(G6PD):c.120+199_120+200insT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.050 ( 80 hom., 118 hem., cov: 20)
Exomes 𝑓: 0.058 ( 0 hom. 1 hem. )
Consequence
G6PD
NM_001360016.2 intron
NM_001360016.2 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.539
Genes affected
G6PD (HGNC:4057): (glucose-6-phosphate dehydrogenase) This gene encodes glucose-6-phosphate dehydrogenase. This protein is a cytosolic enzyme encoded by a housekeeping X-linked gene whose main function is to produce NADPH, a key electron donor in the defense against oxidizing agents and in reductive biosynthetic reactions. G6PD is remarkable for its genetic diversity. Many variants of G6PD, mostly produced from missense mutations, have been described with wide ranging levels of enzyme activity and associated clinical symptoms. G6PD deficiency may cause neonatal jaundice, acute hemolysis, or severe chronic non-spherocytic hemolytic anemia. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
IKBKG (HGNC:5961): (inhibitor of nuclear factor kappa B kinase regulatory subunit gamma) This gene encodes the regulatory subunit of the inhibitor of kappaB kinase (IKK) complex, which activates NF-kappaB resulting in activation of genes involved in inflammation, immunity, cell survival, and other pathways. Mutations in this gene result in incontinentia pigmenti, hypohidrotic ectodermal dysplasia, and several other types of immunodeficiencies. A pseudogene highly similar to this locus is located in an adjacent region of the X chromosome. [provided by RefSeq, Mar 2016]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP6
Variant X-154545836-C-CA is Benign according to our data. Variant chrX-154545836-C-CA is described in ClinVar as [Benign]. Clinvar id is 1246459.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
G6PD | NM_001360016.2 | c.120+199_120+200insT | intron_variant | ENST00000393562.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
G6PD | ENST00000393562.10 | c.120+199_120+200insT | intron_variant | 1 | NM_001360016.2 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0498 AC: 1839AN: 36934Hom.: 79 Cov.: 20 AF XY: 0.0155 AC XY: 120AN XY: 7756
GnomAD3 genomes
AF:
AC:
1839
AN:
36934
Hom.:
Cov.:
20
AF XY:
AC XY:
120
AN XY:
7756
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.0579 AC: 13213AN: 228332Hom.: 0 Cov.: 0 AF XY: 0.0000167 AC XY: 1AN XY: 59726
GnomAD4 exome
AF:
AC:
13213
AN:
228332
Hom.:
Cov.:
0
AF XY:
AC XY:
1
AN XY:
59726
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.0497 AC: 1836AN: 36942Hom.: 80 Cov.: 20 AF XY: 0.0152 AC XY: 118AN XY: 7752
GnomAD4 genome
AF:
AC:
1836
AN:
36942
Hom.:
Cov.:
20
AF XY:
AC XY:
118
AN XY:
7752
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Anemia, nonspherocytic hemolytic, due to G6PD deficiency Benign:1
Benign, criteria provided, single submitter | curation | Dunham Lab, University of Washington | Aug 12, 2022 | Variant found at a frequency of 5.5% in gnomAD (BA1) and previously interpreted as benign (BP6). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 06, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at