chr18-23136294-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001100619.3(CABLES1):c.532G>A(p.Glu178Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00919 in 1,389,104 control chromosomes in the GnomAD database, including 86 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001100619.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CABLES1 | NM_001100619.3 | c.532G>A | p.Glu178Lys | missense_variant | 1/10 | ENST00000256925.12 | |
CABLES1 | NM_001256438.1 | c.-137+1624G>A | intron_variant | ||||
CABLES1 | NR_023359.2 | n.88+1643G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CABLES1 | ENST00000256925.12 | c.532G>A | p.Glu178Lys | missense_variant | 1/10 | 1 | NM_001100619.3 | ||
CABLES1 | ENST00000400473.6 | c.-137+1624G>A | intron_variant | 2 | P1 | ||||
CABLES1 | ENST00000580153.5 | c.-220-230G>A | intron_variant | 5 | |||||
CABLES1 | ENST00000579963.5 | c.-137+1643G>A | intron_variant, NMD_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00683 AC: 1036AN: 151618Hom.: 11 Cov.: 33
GnomAD3 exomes AF: 0.0138 AC: 224AN: 16268Hom.: 4 AF XY: 0.0131 AC XY: 122AN XY: 9282
GnomAD4 exome AF: 0.00948 AC: 11725AN: 1237376Hom.: 75 Cov.: 32 AF XY: 0.00927 AC XY: 5604AN XY: 604302
GnomAD4 genome AF: 0.00682 AC: 1035AN: 151728Hom.: 11 Cov.: 33 AF XY: 0.00744 AC XY: 552AN XY: 74154
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2024 | CABLES1: PP2, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at