chrX-18893636-T-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_000292.3(PHKA2):āc.3557A>Cā(p.Asp1186Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000456 in 1,097,315 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 5 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Consequence
NM_000292.3 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 |
---|---|---|---|---|---|---|---|
PHKA2 | NM_000292.3 | c.3557A>C | p.Asp1186Ala | missense_variant | 33/33 | ENST00000379942.5 | |
PHKA2-AS1 | NR_029379.1 | n.467+298T>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PHKA2 | ENST00000379942.5 | c.3557A>C | p.Asp1186Ala | missense_variant | 33/33 | 1 | NM_000292.3 | P1 | |
PHKA2-AS1 | ENST00000452900.5 | n.467+298T>G | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes Cov.: 24
GnomAD4 exome AF: 0.00000456 AC: 5AN: 1097315Hom.: 0 Cov.: 30 AF XY: 0.0000138 AC XY: 5AN XY: 362685
GnomAD4 genome Cov.: 24
ClinVar
Submissions by phenotype
Glycogen storage disease IXa1 Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | Zotz-Klimas Genetics Lab, MVZ Zotz Klimas | Nov 24, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.