chr1-9245386-A-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_004285.4(H6PD):c.452A>C(p.Asp151Ala) variant causes a missense change. The variant allele was found at a frequency of 0.137 in 1,614,012 control chromosomes in the GnomAD database, including 16,395 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Genomes: 𝑓 0.10 ( 1128 hom., cov: 32)
Exomes 𝑓: 0.14 ( 15267 hom. )
Consequence
H6PD
NM_004285.4 missense
NM_004285.4 missense
Scores
1
7
10
Clinical Significance
Conservation
PhyloP100: 5.79
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0024963915).
BP6
?
Variant 1-9245386-A-C is Benign according to our data. Variant chr1-9245386-A-C is described in ClinVar as [Benign]. Clinvar id is 1601522.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
H6PD | NM_004285.4 | c.452A>C | p.Asp151Ala | missense_variant | 2/5 | ENST00000377403.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
H6PD | ENST00000377403.7 | c.452A>C | p.Asp151Ala | missense_variant | 2/5 | 1 | NM_004285.4 | P1 | |
H6PD | ENST00000602477.1 | c.485A>C | p.Asp162Ala | missense_variant | 2/5 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.105 AC: 15926AN: 152124Hom.: 1128 Cov.: 32
GnomAD3 genomes
?
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GnomAD3 exomes AF: 0.118 AC: 29595AN: 251168Hom.: 2159 AF XY: 0.125 AC XY: 17023AN XY: 135824
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GnomAD4 exome AF: 0.140 AC: 204862AN: 1461770Hom.: 15267 Cov.: 36 AF XY: 0.142 AC XY: 103089AN XY: 727184
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GnomAD4 genome ? AF: 0.105 AC: 15917AN: 152242Hom.: 1128 Cov.: 32 AF XY: 0.103 AC XY: 7682AN XY: 74446
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14571
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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 | Jan 25, 2024 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
Cadd
Uncertain
Dann
Uncertain
DEOGEN2
Uncertain
D;D
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T;T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;.
MutationTaster
Benign
P
PrimateAI
Benign
T
PROVEAN
Uncertain
D;.
REVEL
Uncertain
Sift
Benign
D;.
Sift4G
Benign
T;T
Polyphen
P;.
Vest4
MPC
ClinPred
T
GERP RS
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