rs41272442
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_017780.4(CHD7):c.3523-35C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0175 in 1,577,700 control chromosomes in the GnomAD database, including 1,345 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.058 ( 702 hom., cov: 32)
Exomes 𝑓: 0.013 ( 643 hom. )
Consequence
CHD7
NM_017780.4 intron
NM_017780.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.524
Genes affected
CHD7 (HGNC:20626): (chromodomain helicase DNA binding protein 7) This gene encodes a protein that contains several helicase family domains. Mutations in this gene have been found in some patients with the CHARGE syndrome. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BP6
?
Variant 8-60830287-C-G is Benign according to our data. Variant chr8-60830287-C-G is described in ClinVar as [Benign]. Clinvar id is 260903.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHD7 | NM_017780.4 | c.3523-35C>G | intron_variant | ENST00000423902.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHD7 | ENST00000423902.7 | c.3523-35C>G | intron_variant | 5 | NM_017780.4 | P1 | |||
CHD7 | ENST00000524602.5 | c.1717-31942C>G | intron_variant | 1 | |||||
CHD7 | ENST00000695853.1 | c.3523-35C>G | intron_variant, NMD_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0578 AC: 8787AN: 152086Hom.: 694 Cov.: 32
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GnomAD3 exomes AF: 0.0199 AC: 4476AN: 224874Hom.: 266 AF XY: 0.0173 AC XY: 2119AN XY: 122386
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GnomAD4 exome AF: 0.0131 AC: 18714AN: 1425496Hom.: 643 Cov.: 30 AF XY: 0.0127 AC XY: 8952AN XY: 707212
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GnomAD4 genome ? AF: 0.0579 AC: 8820AN: 152204Hom.: 702 Cov.: 32 AF XY: 0.0567 AC XY: 4223AN XY: 74432
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at