rs201083157
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 1P and 9B. PP2BP4_StrongBP6BS2
The NM_017780.4(CHD7):c.6250A>G(p.Ser2084Gly) variant causes a missense change. The variant allele was found at a frequency of 0.0000496 in 1,613,916 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S2084N) has been classified as Uncertain significance.
Frequency
Consequence
NM_017780.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHD7 | NM_017780.4 | c.6250A>G | p.Ser2084Gly | missense_variant | 31/38 | ENST00000423902.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHD7 | ENST00000423902.7 | c.6250A>G | p.Ser2084Gly | missense_variant | 31/38 | 5 | NM_017780.4 | P1 | |
CHD7 | ENST00000524602.5 | c.1717-9254A>G | intron_variant | 1 | |||||
CHD7 | ENST00000695853.1 | c.6250A>G | p.Ser2084Gly | missense_variant, NMD_transcript_variant | 31/37 |
Frequencies
GnomAD3 genomes ? AF: 0.000270 AC: 41AN: 152086Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000642 AC: 16AN: 249196Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135190
GnomAD4 exome AF: 0.0000260 AC: 38AN: 1461712Hom.: 0 Cov.: 32 AF XY: 0.0000165 AC XY: 12AN XY: 727138
GnomAD4 genome ? AF: 0.000276 AC: 42AN: 152204Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74422
ClinVar
Submissions by phenotype
CHARGE syndrome Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 16, 2024 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Feb 08, 2013 | - - |
Ventricular septal defect;C1384666:Hearing impairment Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | New York Genome Center | May 24, 2019 | - - |
CHD7-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 22, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 21, 2020 | This variant is associated with the following publications: (PMID: 21158681) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at