6-43041026-C-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_014780.5(CUL7):c.3695G>A(p.Arg1232Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0015 in 1,613,856 control chromosomes in the GnomAD database, including 48 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_014780.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00147 AC: 224AN: 152208Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.00277 AC: 695AN: 250760Hom.: 17 AF XY: 0.00265 AC XY: 359AN XY: 135538
GnomAD4 exome AF: 0.00150 AC: 2196AN: 1461648Hom.: 45 Cov.: 32 AF XY: 0.00152 AC XY: 1106AN XY: 727080
GnomAD4 genome AF: 0.00147 AC: 224AN: 152208Hom.: 3 Cov.: 32 AF XY: 0.00126 AC XY: 94AN XY: 74348
ClinVar
Submissions by phenotype
not specified Benign:1
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CUL7-related disorder Benign:1
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). -
3M syndrome 1 Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at