chr8-60820036-T-G
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_017780.4(CHD7):āc.2643T>Gā(p.Tyr881Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (ā ). Synonymous variant affecting the same amino acid position (i.e. Y881Y) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_017780.4 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHD7 | NM_017780.4 | c.2643T>G | p.Tyr881Ter | stop_gained | 9/38 | ENST00000423902.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHD7 | ENST00000423902.7 | c.2643T>G | p.Tyr881Ter | stop_gained | 9/38 | 5 | NM_017780.4 | P1 | |
CHD7 | ENST00000524602.5 | c.1716+38986T>G | intron_variant | 1 | |||||
CHD7 | ENST00000525508.1 | c.2643T>G | p.Tyr881Ter | stop_gained | 8/12 | 5 | |||
CHD7 | ENST00000695853.1 | c.2643T>G | p.Tyr881Ter | stop_gained, NMD_transcript_variant | 9/37 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 151720Hom.: 0 Cov.: 32 FAILED QC
GnomAD4 exome Cov.: 30
GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 151720Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74120
ClinVar
Submissions by phenotype
CHARGE syndrome Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Feb 08, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at