X-85255300-ATTG-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PM4_Supporting
The NM_001330574.2(ZNF711):c.127_129delGTT(p.Val43del) variant causes a conservative inframe deletion change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000911 in 1,097,980 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_001330574.2 conservative_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF711 | ENST00000674551.1 | c.127_129delGTT | p.Val43del | conservative_inframe_deletion | Exon 5 of 11 | NM_001330574.2 | ENSP00000502839.1 | |||
ZNF711 | ENST00000360700.4 | c.127_129delGTT | p.Val43del | conservative_inframe_deletion | Exon 4 of 10 | 1 | ENSP00000353922.4 | |||
ZNF711 | ENST00000276123.7 | c.127_129delGTT | p.Val43del | conservative_inframe_deletion | Exon 5 of 10 | 1 | ENSP00000276123.3 | |||
ZNF711 | ENST00000373165.7 | c.127_129delGTT | p.Val43del | conservative_inframe_deletion | Exon 4 of 9 | 1 | ENSP00000362260.3 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD4 exome AF: 9.11e-7 AC: 1AN: 1097980Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 363340
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
not provided Uncertain:2
- -
Not observed in large population cohorts (Lek et al., 2016); In-frame deletion of 1 amino acid in a non-repeat region; In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Has not been previously published as pathogenic or benign to our knowledge -
Intellectual disability, X-linked 97 Other:1
Variant interpreted as Uncertain significance and reported on 12-05-2019 by Lab or GTR ID 26957. Assertions are reported exactly as they appear on the patient provided laboratory report. GenomeConnect does not attempt to reinterpret the variant. The IDDRC-CTSA National Brain Gene Registry (BGR ) is a study funded by the U.S. National Center for Advancing Translational Sciences (NCATS) and includes 13 Intellectual and Developmental Disability Research Center (IDDRC) institutions. The study is led by Principal Investigator John Constantino MD PhD from Washington University. The BGR is a data commons of gene variants paired with subject clinical information. This database helps scientists learn more about genetic changes and their impact on the brain and behavior. Participation in the Brain Gene Registry requires participation in GenomeConnect. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at