rs41312172
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_017780.4(CHD7):c.6282A>G(p.Gly2094Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00668 in 1,613,962 control chromosomes in the GnomAD database, including 36 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_017780.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
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CHD7 | ENST00000423902.7 | c.6282A>G | p.Gly2094Gly | synonymous_variant | Exon 31 of 38 | 5 | NM_017780.4 | ENSP00000392028.1 | ||
CHD7 | ENST00000524602.5 | c.1717-9222A>G | intron_variant | Intron 2 of 4 | 1 | ENSP00000437061.1 | ||||
CHD7 | ENST00000695853.1 | n.6282A>G | non_coding_transcript_exon_variant | Exon 31 of 37 | ENSP00000512218.1 |
Frequencies
GnomAD3 genomes AF: 0.00467 AC: 710AN: 152132Hom.: 5 Cov.: 32
GnomAD3 exomes AF: 0.00436 AC: 1087AN: 249154Hom.: 4 AF XY: 0.00456 AC XY: 617AN XY: 135170
GnomAD4 exome AF: 0.00689 AC: 10066AN: 1461712Hom.: 31 Cov.: 32 AF XY: 0.00676 AC XY: 4917AN XY: 727138
GnomAD4 genome AF: 0.00466 AC: 710AN: 152250Hom.: 5 Cov.: 32 AF XY: 0.00459 AC XY: 342AN XY: 74446
ClinVar
Submissions by phenotype
not specified Benign:7
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p.Gly2094Gly in exon 31 of CHD7: This variant is not expected to have clinical s ignificance because it does not alter an amino acid residue, is not located with in the splice consensus sequence, and has been identified in 0.65% (432/66718) o f European chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.br oadinstitute.org; dbSNP rs41312172). -
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not provided Benign:3
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CHD7: BP4, BP7, BS2 -
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CHARGE syndrome Benign:1
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Inborn genetic diseases Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
CHARGE syndrome;C3552553:Hypogonadotropic hypogonadism 5 with or without anosmia Benign:1
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Hypogonadotropic hypogonadism 5 with or without anosmia Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at