chr15-65196790-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_003613.4(CILP):c.3496G>A(p.Gly1166Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.805 in 1,594,238 control chromosomes in the GnomAD database, including 520,488 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_003613.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CILP | NM_003613.4 | c.3496G>A | p.Gly1166Ser | missense_variant | 9/9 | ENST00000261883.6 | |
CILP | XM_017022679.2 | c.3424G>A | p.Gly1142Ser | missense_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CILP | ENST00000261883.6 | c.3496G>A | p.Gly1166Ser | missense_variant | 9/9 | 1 | NM_003613.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.757 AC: 115106AN: 151956Hom.: 44525 Cov.: 32
GnomAD3 exomes AF: 0.827 AC: 196319AN: 237474Hom.: 82066 AF XY: 0.831 AC XY: 106232AN XY: 127848
GnomAD4 exome AF: 0.810 AC: 1168820AN: 1442164Hom.: 475925 Cov.: 64 AF XY: 0.813 AC XY: 581228AN XY: 714944
GnomAD4 genome AF: 0.758 AC: 115202AN: 152074Hom.: 44563 Cov.: 32 AF XY: 0.763 AC XY: 56707AN XY: 74342
ClinVar
Submissions by phenotype
CILP-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 16, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at