18-23136201-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001100619.3(CABLES1):c.439C>T(p.Pro147Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000408 in 1,251,300 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P147L) has been classified as Uncertain significance.
Frequency
Consequence
NM_001100619.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CABLES1 | NM_001100619.3 | c.439C>T | p.Pro147Ser | missense_variant | 1/10 | ENST00000256925.12 | |
CABLES1 | NM_001256438.1 | c.-137+1531C>T | intron_variant | ||||
CABLES1 | NR_023359.2 | n.88+1550C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CABLES1 | ENST00000256925.12 | c.439C>T | p.Pro147Ser | missense_variant | 1/10 | 1 | NM_001100619.3 | ||
CABLES1 | ENST00000400473.6 | c.-137+1531C>T | intron_variant | 2 | P1 | ||||
CABLES1 | ENST00000580153.5 | c.-220-323C>T | intron_variant | 5 | |||||
CABLES1 | ENST00000579963.5 | c.-137+1550C>T | intron_variant, NMD_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000198 AC: 30AN: 151590Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.0000191 AC: 21AN: 1099710Hom.: 0 Cov.: 32 AF XY: 0.0000229 AC XY: 12AN XY: 523150
GnomAD4 genome ? AF: 0.000198 AC: 30AN: 151590Hom.: 0 Cov.: 33 AF XY: 0.000176 AC XY: 13AN XY: 73996
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 13, 2024 | The c.439C>T (p.P147S) alteration is located in exon 1 (coding exon 1) of the CABLES1 gene. This alteration results from a C to T substitution at nucleotide position 439, causing the proline (P) at amino acid position 147 to be replaced by a serine (S). 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