rs2073711
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_003613.4(CILP):āc.1184T>Cā(p.Ile395Thr) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.603 in 1,534,168 control chromosomes in the GnomAD database, including 285,531 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Consequence
NM_003613.4 missense, splice_region
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.1184T>C | p.Ile395Thr | missense_variant, splice_region_variant | 8/9 | ENST00000261883.6 | |
CILP | XM_017022679.2 | c.1112T>C | p.Ile371Thr | missense_variant, splice_region_variant | 7/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CILP | ENST00000261883.6 | c.1184T>C | p.Ile395Thr | missense_variant, splice_region_variant | 8/9 | 1 | NM_003613.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.605 AC: 91854AN: 151886Hom.: 28480 Cov.: 31
GnomAD3 exomes AF: 0.562 AC: 109049AN: 193914Hom.: 32549 AF XY: 0.559 AC XY: 58641AN XY: 104964
GnomAD4 exome AF: 0.603 AC: 833067AN: 1382164Hom.: 257024 Cov.: 44 AF XY: 0.598 AC XY: 408349AN XY: 683040
GnomAD4 genome ? AF: 0.605 AC: 91933AN: 152004Hom.: 28507 Cov.: 31 AF XY: 0.597 AC XY: 44329AN XY: 74286
ClinVar
Submissions by phenotype
CILP-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 17, 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). - |
Lumbar disc disease, susceptibility to Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Jun 01, 2005 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at