1-9245120-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2
The NM_004285.4(H6PD):c.186C>T(p.Phe62=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00138 in 1,614,200 control chromosomes in the GnomAD database, including 25 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0075 ( 12 hom., cov: 32)
Exomes 𝑓: 0.00075 ( 13 hom. )
Consequence
H6PD
NM_004285.4 synonymous
NM_004285.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.17
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 -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.36).
BP6
?
Variant 1-9245120-C-T is Benign according to our data. Variant chr1-9245120-C-T is described in ClinVar as [Benign]. Clinvar id is 777319.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=1.17 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0075 (1142/152322) while in subpopulation AFR AF= 0.026 (1081/41566). AF 95% confidence interval is 0.0247. There are 12 homozygotes in gnomad4. There are 545 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 12 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
H6PD | NM_004285.4 | c.186C>T | p.Phe62= | synonymous_variant | 2/5 | ENST00000377403.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
H6PD | ENST00000377403.7 | c.186C>T | p.Phe62= | synonymous_variant | 2/5 | 1 | NM_004285.4 | P1 | |
H6PD | ENST00000602477.1 | c.219C>T | p.Phe73= | synonymous_variant | 2/5 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00750 AC: 1142AN: 152204Hom.: 12 Cov.: 32
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GnomAD3 exomes AF: 0.00182 AC: 457AN: 251400Hom.: 2 AF XY: 0.00132 AC XY: 179AN XY: 135872
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GnomAD4 exome AF: 0.000746 AC: 1091AN: 1461878Hom.: 13 Cov.: 34 AF XY: 0.000601 AC XY: 437AN XY: 727244
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GnomAD4 genome ? AF: 0.00750 AC: 1142AN: 152322Hom.: 12 Cov.: 32 AF XY: 0.00732 AC XY: 545AN XY: 74490
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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 07, 2023 | - - |
Computational scores
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Name
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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