chr4-1212284-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001012614.2(CTBP1):c.1246G>A(p.Val416Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000843 in 1,008,162 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_001012614.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000787 AC: 11AN: 139784Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000852 AC: 74AN: 868378Hom.: 0 Cov.: 36 AF XY: 0.0000695 AC XY: 30AN XY: 431820
GnomAD4 genome AF: 0.0000787 AC: 11AN: 139784Hom.: 0 Cov.: 32 AF XY: 0.0000739 AC XY: 5AN XY: 67614
ClinVar
Submissions by phenotype
not provided Uncertain:2
This sequence change replaces valine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 427 of the CTBP1 protein (p.Val427Ile). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with CTBP1-related conditions. ClinVar contains an entry for this variant (Variation ID: 2440596). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
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Hypotonia, ataxia, developmental delay, and tooth enamel defect syndrome Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at