chr11-125625944-A-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The ENST00000427383.6(CHEK1):c.184A>T(p.Thr62Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000124 in 702,596 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000427383.6 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 |
---|---|---|---|---|---|---|---|
CHEK1 | NM_001114122.3 | c.-89A>T | 5_prime_UTR_variant | 1/13 | ENST00000438015.7 | ||
LOC118567325 | NR_170378.1 | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHEK1 | ENST00000438015.7 | c.-89A>T | 5_prime_UTR_variant | 1/13 | 5 | NM_001114122.3 | P1 | ||
ENST00000686400.2 | upstream_gene_variant |
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152216Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000695 AC: 9AN: 129418Hom.: 0 AF XY: 0.0000565 AC XY: 4AN XY: 70748
GnomAD4 exome AF: 0.000127 AC: 70AN: 550262Hom.: 0 Cov.: 0 AF XY: 0.000124 AC XY: 37AN XY: 297862
GnomAD4 genome AF: 0.000112 AC: 17AN: 152334Hom.: 0 Cov.: 32 AF XY: 0.0000671 AC XY: 5AN XY: 74492
ClinVar
Submissions by phenotype
CHEK1-related disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 08, 2023 | The CHEK1 c.184A>T variant is predicted to result in the amino acid substitution p.Thr62Ser. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.016% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/11-125495839-A-T). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at