rs117554009
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP7BS2
The NM_004703.6(RABEP1):c.2376C>A(p.Thr792Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000325 in 1,609,600 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.00038 ( 1 hom., cov: 33)
Exomes 𝑓: 0.00032 ( 3 hom. )
Consequence
RABEP1
NM_004703.6 synonymous
NM_004703.6 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.14
Genes affected
RABEP1 (HGNC:17677): (rabaptin, RAB GTPase binding effector protein 1) Enables protein domain specific binding activity and protein homodimerization activity. Involved in vesicle-mediated transport. Located in endocytic vesicle and endosome. Part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]
NUP88 (HGNC:8067): (nucleoporin 88) The nuclear pore complex is a massive structure that extends across the nuclear envelope, forming a gateway that regulates the flow of macromolecules between the nucleus and the cytoplasm. Nucleoporins, a family of 50 to 100 proteins, are the main components of the nuclear pore complex in eukaryotic cells. The protein encoded by this gene belongs to the nucleoporin family and is associated with the oncogenic nucleoporin CAN/Nup214 in a dynamic subcomplex. This protein is also overexpressed in a large number of malignant neoplasms and precancerous dysplasias. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Mar 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.53).
BP7
Synonymous conserved (PhyloP=-1.13 with no splicing effect.
BS2
High Homozygotes in GnomAdExome4 at 3 gene
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000381 AC: 58AN: 152116Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.00109 AC: 268AN: 245116Hom.: 2 AF XY: 0.000850 AC XY: 113AN XY: 132876
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GnomAD4 exome AF: 0.000319 AC: 465AN: 1457366Hom.: 3 Cov.: 29 AF XY: 0.000306 AC XY: 222AN XY: 724736
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GnomAD4 genome AF: 0.000381 AC: 58AN: 152234Hom.: 1 Cov.: 33 AF XY: 0.000457 AC XY: 34AN XY: 74420
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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