chrX-18893503-C-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_ModerateBP6_ModerateBP7
The NM_000292.3(PHKA2):āc.3690G>Cā(p.Ser1230=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000909 in 1,209,519 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_000292.3 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PHKA2 | NM_000292.3 | c.3690G>C | p.Ser1230= | synonymous_variant | 33/33 | ENST00000379942.5 | |
PHKA2-AS1 | NR_029379.1 | n.467+165C>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PHKA2 | ENST00000379942.5 | c.3690G>C | p.Ser1230= | synonymous_variant | 33/33 | 1 | NM_000292.3 | P1 | |
PHKA2-AS1 | ENST00000452900.5 | n.467+165C>G | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000447 AC: 5AN: 111782Hom.: 0 Cov.: 23 AF XY: 0.0000294 AC XY: 1AN XY: 33958
GnomAD3 exomes AF: 0.0000109 AC: 2AN: 183504Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67930
GnomAD4 exome AF: 0.00000547 AC: 6AN: 1097737Hom.: 0 Cov.: 30 AF XY: 0.00000275 AC XY: 1AN XY: 363101
GnomAD4 genome AF: 0.0000447 AC: 5AN: 111782Hom.: 0 Cov.: 23 AF XY: 0.0000294 AC XY: 1AN XY: 33958
ClinVar
Submissions by phenotype
Glycogen storage disease IXa1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Apr 17, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at