rs782159405
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_002637.4(PHKA1):c.2405G>A(p.Arg802Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000083 in 1,204,775 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 31 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R802W) has been classified as Uncertain significance.
Frequency
Consequence
NM_002637.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PHKA1 | NM_002637.4 | c.2405G>A | p.Arg802Gln | missense_variant | 22/32 | ENST00000373542.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PHKA1 | ENST00000373542.9 | c.2405G>A | p.Arg802Gln | missense_variant | 22/32 | 1 | NM_002637.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000135 AC: 15AN: 111312Hom.: 0 Cov.: 22 AF XY: 0.000179 AC XY: 6AN XY: 33514
GnomAD3 exomes AF: 0.000241 AC: 44AN: 182911Hom.: 0 AF XY: 0.000266 AC XY: 18AN XY: 67559
GnomAD4 exome AF: 0.0000777 AC: 85AN: 1093410Hom.: 0 Cov.: 28 AF XY: 0.0000696 AC XY: 25AN XY: 359140
GnomAD4 genome ? AF: 0.000135 AC: 15AN: 111365Hom.: 0 Cov.: 22 AF XY: 0.000179 AC XY: 6AN XY: 33577
ClinVar
Submissions by phenotype
Spinocerebellar ataxia, X-linked Uncertain:1
Uncertain significance, no assertion criteria provided | case-control | Vavilov Institute of General Genetics RAS, Laboratory of Evolutional Genomics | - | - - |
Glycogen storage disease IXd Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 19, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at