NM_000292.3:c.849T>A
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_000292.3(PHKA2):c.849T>A(p.Ile283Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00293 in 1,208,421 control chromosomes in the GnomAD database, including 45 homozygotes. There are 995 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_000292.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0130 AC: 1462AN: 112437Hom.: 23 Cov.: 23 AF XY: 0.0114 AC XY: 394AN XY: 34591
GnomAD3 exomes AF: 0.00428 AC: 786AN: 183449Hom.: 12 AF XY: 0.00271 AC XY: 184AN XY: 67887
GnomAD4 exome AF: 0.00189 AC: 2073AN: 1095930Hom.: 21 Cov.: 29 AF XY: 0.00166 AC XY: 601AN XY: 361332
GnomAD4 genome AF: 0.0130 AC: 1464AN: 112491Hom.: 24 Cov.: 23 AF XY: 0.0114 AC XY: 394AN XY: 34655
ClinVar
Submissions by phenotype
not specified Benign:2
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
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not provided Benign:2
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Glycogen storage disease IXa1 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at