18-23135929-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001100619.3(CABLES1):c.167G>T(p.Arg56Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000208 in 1,107,168 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001100619.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CABLES1 | NM_001100619.3 | c.167G>T | p.Arg56Leu | missense_variant | 1/10 | ENST00000256925.12 | |
CABLES1 | NM_001256438.1 | c.-137+1259G>T | intron_variant | ||||
CABLES1 | NR_023359.2 | n.88+1278G>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CABLES1 | ENST00000256925.12 | c.167G>T | p.Arg56Leu | missense_variant | 1/10 | 1 | NM_001100619.3 | ||
CABLES1 | ENST00000400473.6 | c.-137+1259G>T | intron_variant | 2 | P1 | ||||
CABLES1 | ENST00000580153.5 | c.-221+384G>T | intron_variant | 5 | |||||
CABLES1 | ENST00000579963.5 | c.-137+1278G>T | intron_variant, NMD_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000813 AC: 12AN: 147522Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000115 AC: 11AN: 959536Hom.: 0 Cov.: 30 AF XY: 0.0000109 AC XY: 5AN XY: 457128
GnomAD4 genome ? AF: 0.0000813 AC: 12AN: 147632Hom.: 0 Cov.: 32 AF XY: 0.0000278 AC XY: 2AN XY: 71902
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 20, 2023 | The c.167G>T (p.R56L) alteration is located in exon 1 (coding exon 1) of the CABLES1 gene. This alteration results from a G to T substitution at nucleotide position 167, causing the arginine (R) at amino acid position 56 to be replaced by a leucine (L). 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