11-68064604-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001277.3(CHKA):c.1153G>A(p.Ala385Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000555 in 1,441,238 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001277.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHKA | NM_001277.3 | c.1153G>A | p.Ala385Thr | missense_variant | 10/12 | ENST00000265689.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHKA | ENST00000265689.9 | c.1153G>A | p.Ala385Thr | missense_variant | 10/12 | 1 | NM_001277.3 | ||
CHKA | ENST00000356135.9 | c.1099G>A | p.Ala367Thr | missense_variant | 9/11 | 1 | P1 | ||
CHKA | ENST00000525155.5 | c.169G>A | p.Ala57Thr | missense_variant, NMD_transcript_variant | 3/6 | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000128 AC: 3AN: 235154Hom.: 0 AF XY: 0.00000787 AC XY: 1AN XY: 127108
GnomAD4 exome AF: 0.00000555 AC: 8AN: 1441238Hom.: 0 Cov.: 28 AF XY: 0.00000698 AC XY: 5AN XY: 716514
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 30, 2021 | The c.1153G>A (p.A385T) alteration is located in exon 10 (coding exon 10) of the CHKA gene. This alteration results from a G to A substitution at nucleotide position 1153, causing the alanine (A) at amino acid position 385 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at