chr2-205113577-G-GGTA
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PVS1_ModeratePM2
The ENST00000406610.7(PARD3B):c.680_680+1insGTA variant causes a splice donor, intron change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000622 in 1,607,334 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000406610.7 splice_donor, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 151978Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000413 AC: 1AN: 242050Hom.: 0 AF XY: 0.00000760 AC XY: 1AN XY: 131584
GnomAD4 exome AF: 0.00000481 AC: 7AN: 1455356Hom.: 0 Cov.: 30 AF XY: 0.00000552 AC XY: 4AN XY: 724160
GnomAD4 genome AF: 0.0000197 AC: 3AN: 151978Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74224
ClinVar
Submissions by phenotype
PARD3B-related disorder Uncertain:1
The PARD3B c.680+1_680+3dupGTA variant is predicted to result in an intronic duplication. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.00090% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/2-205978301-G-GGTA). Other variants predicted to impact splicing have been reported in association with neurodevelopmental phenotypes (Stessman et al. 2017. PubMed ID: 28191889). 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