rs201381395
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_017780.4(CHD7):c.2835+24A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000152 in 1,613,280 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00076 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000090 ( 1 hom. )
Consequence
CHD7
NM_017780.4 intron
NM_017780.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.96
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 -16 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BP6
?
Variant 8-60821951-A-T is Benign according to our data. Variant chr8-60821951-A-T is described in ClinVar as [Likely_benign]. Clinvar id is 260901.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
?
High AC in GnomAd4 at 115 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHD7 | NM_017780.4 | c.2835+24A>T | intron_variant | ENST00000423902.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHD7 | ENST00000423902.7 | c.2835+24A>T | intron_variant | 5 | NM_017780.4 | P1 | |||
CHD7 | ENST00000524602.5 | c.1717-40278A>T | intron_variant | 1 | |||||
CHD7 | ENST00000525508.1 | c.2835+24A>T | intron_variant | 5 | |||||
CHD7 | ENST00000695853.1 | c.2835+24A>T | intron_variant, NMD_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.000756 AC: 115AN: 152090Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000226 AC: 56AN: 248120Hom.: 0 AF XY: 0.000163 AC XY: 22AN XY: 134602
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GnomAD4 exome AF: 0.0000897 AC: 131AN: 1461074Hom.: 1 Cov.: 32 AF XY: 0.0000743 AC XY: 54AN XY: 726766
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GnomAD4 genome ? AF: 0.000756 AC: 115AN: 152206Hom.: 0 Cov.: 32 AF XY: 0.000793 AC XY: 59AN XY: 74416
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 20, 2020 | - - |
Computational scores
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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