chr1-9245334-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_004285.4(H6PD):c.400C>T(p.Arg134Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000615 in 1,614,170 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_004285.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
H6PD | NM_004285.4 | c.400C>T | p.Arg134Trp | missense_variant | 2/5 | ENST00000377403.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
H6PD | ENST00000377403.7 | c.400C>T | p.Arg134Trp | missense_variant | 2/5 | 1 | NM_004285.4 | P1 | |
H6PD | ENST00000602477.1 | c.433C>T | p.Arg145Trp | missense_variant | 2/5 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00122 AC: 185AN: 152202Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00138 AC: 346AN: 251340Hom.: 1 AF XY: 0.00127 AC XY: 172AN XY: 135882
GnomAD4 exome AF: 0.000552 AC: 807AN: 1461850Hom.: 2 Cov.: 34 AF XY: 0.000538 AC XY: 391AN XY: 727228
GnomAD4 genome ? AF: 0.00121 AC: 185AN: 152320Hom.: 0 Cov.: 32 AF XY: 0.00172 AC XY: 128AN XY: 74482
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 06, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at