chr1-9245473-A-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_004285.4(H6PD):c.539A>G(p.His180Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000426 in 1,613,952 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_004285.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
H6PD | NM_004285.4 | c.539A>G | p.His180Arg | missense_variant | 2/5 | ENST00000377403.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
H6PD | ENST00000377403.7 | c.539A>G | p.His180Arg | missense_variant | 2/5 | 1 | NM_004285.4 | P1 | |
H6PD | ENST00000602477.1 | c.572A>G | p.His191Arg | missense_variant | 2/5 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000362 AC: 55AN: 152136Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000442 AC: 111AN: 251148Hom.: 1 AF XY: 0.000361 AC XY: 49AN XY: 135836
GnomAD4 exome AF: 0.000432 AC: 632AN: 1461816Hom.: 0 Cov.: 34 AF XY: 0.000430 AC XY: 313AN XY: 727216
GnomAD4 genome ? AF: 0.000362 AC: 55AN: 152136Hom.: 1 Cov.: 32 AF XY: 0.000296 AC XY: 22AN XY: 74320
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 17, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at