chr1-9246952-TC-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_004285.4(H6PD):c.628-6del variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000694 in 1,554,890 control chromosomes in the GnomAD database, including 4 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0028 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00046 ( 3 hom. )
Consequence
H6PD
NM_004285.4 splice_polypyrimidine_tract, intron
NM_004285.4 splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.00
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 Likely_benign. Variant got -6 ACMG points.
BP6
?
Variant 1-9246952-TC-T is Benign according to our data. Variant chr1-9246952-TC-T is described in ClinVar as [Benign]. Clinvar id is 1987851.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAdExome at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
H6PD | NM_004285.4 | c.628-6del | splice_polypyrimidine_tract_variant, intron_variant | ENST00000377403.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
H6PD | ENST00000377403.7 | c.628-6del | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_004285.4 | P1 | |||
H6PD | ENST00000602477.1 | c.661-6del | splice_polypyrimidine_tract_variant, intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00280 AC: 422AN: 150826Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.000786 AC: 196AN: 249472Hom.: 2 AF XY: 0.000614 AC XY: 83AN XY: 135148
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GnomAD4 exome AF: 0.000464 AC: 652AN: 1403950Hom.: 3 Cov.: 26 AF XY: 0.000415 AC XY: 291AN XY: 701202
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GnomAD4 genome ? AF: 0.00283 AC: 427AN: 150940Hom.: 1 Cov.: 32 AF XY: 0.00295 AC XY: 217AN XY: 73616
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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 14, 2022 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at