chrX-16869561-T-G
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_002893.4(RBBP7):c.17-341A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000335 in 1,164,727 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 15 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0000090 ( 0 hom., 0 hem., cov: 22)
Exomes 𝑓: 0.000036 ( 0 hom. 15 hem. )
Consequence
RBBP7
NM_002893.4 intron
NM_002893.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.74
Genes affected
RBBP7 (HGNC:9890): (RB binding protein 7, chromatin remodeling factor) This protein is a ubiquitously expressed nuclear protein and belongs to a highly conserved subfamily of WD-repeat proteins. It is found among several proteins that binds directly to retinoblastoma protein, which regulates cell proliferation. The encoded protein is found in many histone deacetylase complexes, including mSin3 co-repressor complex. It is also present in protein complexes involved in chromatin assembly. This protein can interact with BRCA1 tumor-suppressor gene and may have a role in the regulation of cell proliferation and differentiation. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
Variant X-16869561-T-G is Benign according to our data. Variant chrX-16869561-T-G is described in ClinVar as [Likely_benign]. Clinvar id is 2660072.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Hemizygotes in GnomAdExome4 at 15 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RBBP7 | NM_002893.4 | c.17-341A>C | intron_variant | ENST00000380087.7 | |||
RBBP7 | NM_001198719.2 | c.81A>C | p.Leu27= | synonymous_variant | 1/12 | ||
RBBP7 | XM_047442291.1 | c.81A>C | p.Leu27= | synonymous_variant | 1/12 | ||
RBBP7 | XM_047442292.1 | c.17-341A>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RBBP7 | ENST00000380087.7 | c.17-341A>C | intron_variant | 1 | NM_002893.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000897 AC: 1AN: 111451Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33667
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GnomAD4 exome AF: 0.0000361 AC: 38AN: 1053276Hom.: 0 Cov.: 31 AF XY: 0.0000435 AC XY: 15AN XY: 344550
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GnomAD4 genome AF: 0.00000897 AC: 1AN: 111451Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33667
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2022 | RBBP7: BP4, BP7 - |
Computational scores
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Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at