15-65197186-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_003613.4(CILP):c.3100C>T(p.Arg1034Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000136 in 1,613,896 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1034H) has been classified as Likely benign.
Frequency
Consequence
NM_003613.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CILP | NM_003613.4 | c.3100C>T | p.Arg1034Cys | missense_variant | 9/9 | ENST00000261883.6 | |
CILP | XM_017022679.2 | c.3028C>T | p.Arg1010Cys | missense_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CILP | ENST00000261883.6 | c.3100C>T | p.Arg1034Cys | missense_variant | 9/9 | 1 | NM_003613.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152164Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 251002Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135730
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461732Hom.: 0 Cov.: 77 AF XY: 0.0000193 AC XY: 14AN XY: 727176
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152164Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 08, 2024 | The c.3100C>T (p.R1034C) alteration is located in exon 9 (coding exon 8) of the CILP gene. This alteration results from a C to T substitution at nucleotide position 3100, causing the arginine (R) at amino acid position 1034 to be replaced by a cysteine (C). 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