chrX-16869637-G-A
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_002893.4(RBBP7):c.16+401C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000482 in 1,037,598 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 22)
Exomes 𝑓: 0.0000048 ( 0 hom. 1 hem. )
Consequence
RBBP7
NM_002893.4 intron
NM_002893.4 intron
Scores
2
3
8
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.12
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 Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RBBP7 | NM_002893.4 | c.16+401C>T | intron_variant | ENST00000380087.7 | |||
RBBP7 | NM_001198719.2 | c.5C>T | p.Ala2Val | missense_variant | 1/12 | ||
RBBP7 | XM_047442291.1 | c.5C>T | p.Ala2Val | missense_variant | 1/12 | ||
RBBP7 | XM_047442292.1 | c.16+401C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RBBP7 | ENST00000380087.7 | c.16+401C>T | intron_variant | 1 | NM_002893.4 | P1 |
Frequencies
GnomAD3 genomes Cov.: 22
GnomAD3 genomes
Cov.:
22
GnomAD4 exome AF: 0.00000482 AC: 5AN: 1037598Hom.: 0 Cov.: 32 AF XY: 0.00000303 AC XY: 1AN XY: 329890
GnomAD4 exome
AF:
AC:
5
AN:
1037598
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Cov.:
32
AF XY:
AC XY:
1
AN XY:
329890
Gnomad4 AFR exome
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GnomAD4 genome Cov.: 22
GnomAD4 genome
Cov.:
22
Bravo
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
M_CAP
Pathogenic
D
MetaRNN
Uncertain
D
MetaSVM
Benign
T
MutationTaster
Benign
D;D;N
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Pathogenic
D
Vest4
MutPred
Gain of stability (P = 0.0144);
MVP
MPC
ClinPred
D
GERP RS
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at