chr7-117719614-G-GTGAT
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_033427.3(CTTNBP2):c.4530_4533dupATCA(p.Leu1512IlefsTer16) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000496 in 1,613,438 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_033427.3 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152180Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250876Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135590
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461258Hom.: 0 Cov.: 30 AF XY: 0.00000413 AC XY: 3AN XY: 726958
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152180Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74336
ClinVar
Submissions by phenotype
CTTNBP2-related disorder Uncertain:1
The CTTNBP2 c.4530_4533dupATCA variant is predicted to result in a frameshift and premature protein termination (p.Leu1512Ilefs*16). To our knowledge, this variant has not been reported in the literature. Only one chain-terminating variant in this gene was previously reported 3' of this location, and that variant was inherited from a parent (unknown phenotype) of the proband (Guo et al. 2018. PubMed ID: 30564305). The c.4530_4533dup variant is reported in 0.0033% of alleles in individuals of South Asian descent in gnomAD (http://gnomad.broadinstitute.org/variant/7-117359668-G-GTGAT). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at