chr11-68120988-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001277.3(CHKA):c.190C>T(p.Pro64Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000017 in 1,120,382 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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.190C>T | p.Pro64Ser | missense_variant | 1/12 | ENST00000265689.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHKA | ENST00000265689.9 | c.190C>T | p.Pro64Ser | missense_variant | 1/12 | 1 | NM_001277.3 | ||
CHKA | ENST00000356135.9 | c.190C>T | p.Pro64Ser | missense_variant | 1/11 | 1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000605 AC: 9AN: 148800Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000103 AC: 10AN: 971582Hom.: 0 Cov.: 27 AF XY: 0.0000109 AC XY: 5AN XY: 457612
GnomAD4 genome AF: 0.0000605 AC: 9AN: 148800Hom.: 0 Cov.: 32 AF XY: 0.0000690 AC XY: 5AN XY: 72498
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 16, 2022 | The c.190C>T (p.P64S) alteration is located in exon 1 (coding exon 1) of the CHKA gene. This alteration results from a C to T substitution at nucleotide position 190, causing the proline (P) at amino acid position 64 to be replaced by a serine (S). 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