chr19-42271919-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001386298.1(CIC):c.136G>A(p.Glu46Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000714 in 399,030 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 7/10 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001386298.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CIC | NM_001386298.1 | c.136G>A | p.Glu46Lys | missense_variant | 2/21 | ENST00000681038.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CIC | ENST00000681038.1 | c.136G>A | p.Glu46Lys | missense_variant | 2/21 | NM_001386298.1 | P1 | ||
CIC | ENST00000572681.6 | c.136G>A | p.Glu46Lys | missense_variant | 2/21 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000605 AC: 92AN: 152176Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.000782 AC: 193AN: 246736Hom.: 0 Cov.: 0 AF XY: 0.000759 AC XY: 95AN XY: 125112
GnomAD4 genome AF: 0.000604 AC: 92AN: 152294Hom.: 0 Cov.: 33 AF XY: 0.000537 AC XY: 40AN XY: 74476
ClinVar
Submissions by phenotype
CIC-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 26, 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). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2024 | CIC: BS1 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at