rs12032814
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_004285.4(H6PD):c.745+88T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 899,800 control chromosomes in the GnomAD database, including 23,554 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.23 ( 4318 hom., cov: 32)
Exomes 𝑓: 0.22 ( 19236 hom. )
Consequence
H6PD
NM_004285.4 intron
NM_004285.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.90
Genes affected
H6PD (HGNC:4795): (hexose-6-phosphate dehydrogenase/glucose 1-dehydrogenase) There are 2 forms of glucose-6-phosphate dehydrogenase. G form is X-linked and H form, encoded by this gene, is autosomally linked. This H form shows activity with other hexose-6-phosphates, especially galactose-6-phosphate, whereas the G form is specific for glucose-6-phosphate. Both forms are present in most tissues, but H form is not found in red cells. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
?
Variant 1-9247171-T-A is Benign according to our data. Variant chr1-9247171-T-A is described in ClinVar as [Likely_benign]. Clinvar id is 191261.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
H6PD | NM_004285.4 | c.745+88T>A | intron_variant | ENST00000377403.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
H6PD | ENST00000377403.7 | c.745+88T>A | intron_variant | 1 | NM_004285.4 | P1 | |||
H6PD | ENST00000602477.1 | c.778+88T>A | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.234 AC: 35397AN: 151302Hom.: 4315 Cov.: 32
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GnomAD4 exome AF: 0.219 AC: 163630AN: 748382Hom.: 19236 AF XY: 0.216 AC XY: 86263AN XY: 399254
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GnomAD4 genome ? AF: 0.234 AC: 35424AN: 151418Hom.: 4318 Cov.: 32 AF XY: 0.231 AC XY: 17069AN XY: 73974
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | research | Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center | Sep 28, 2016 | - - |
Cortisone reductase deficiency 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Mendelics | May 28, 2019 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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