chrX-18893628-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_000292.3(PHKA2):c.3565G>A(p.Glu1189Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000628 in 1,210,198 control chromosomes in the GnomAD database, including 1 homozygotes. There are 44 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. E1189E) has been classified as Likely benign.
Frequency
Consequence
NM_000292.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PHKA2 | NM_000292.3 | c.3565G>A | p.Glu1189Lys | missense_variant | 33/33 | ENST00000379942.5 | |
PHKA2-AS1 | NR_029379.1 | n.467+290C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PHKA2 | ENST00000379942.5 | c.3565G>A | p.Glu1189Lys | missense_variant | 33/33 | 1 | NM_000292.3 | P1 | |
PHKA2-AS1 | ENST00000452900.5 | n.467+290C>T | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000888 AC: 1AN: 112583Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 34733
GnomAD3 exomes AF: 0.000203 AC: 37AN: 182425Hom.: 0 AF XY: 0.000356 AC XY: 24AN XY: 67383
GnomAD4 exome AF: 0.0000683 AC: 75AN: 1097615Hom.: 1 Cov.: 29 AF XY: 0.000121 AC XY: 44AN XY: 362981
GnomAD4 genome ? AF: 0.00000888 AC: 1AN: 112583Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 34733
ClinVar
Submissions by phenotype
PHKA2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 17, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at