22-21547775-A-ACACCTG
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Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM4BP6BA1
The NM_001128633.2(RIMBP3C):c.3201_3202insCAGGTG(p.Gln1066_Val1067dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: 𝑓 0.40 ( 62 hom., cov: 0)
Exomes 𝑓: 0.32 ( 1955 hom. )
Failed GnomAD Quality Control
Consequence
RIMBP3C
NM_001128633.2 inframe_insertion
NM_001128633.2 inframe_insertion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.0600
Genes affected
RIMBP3C (HGNC:33892): (RIMS binding protein 3C) Predicted to enable benzodiazepine receptor binding activity. Predicted to be involved in fertilization and spermatid development. Predicted to be located in cytoplasm. Predicted to be active in nucleus. Predicted to colocalize with manchette. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
PM4
Nonframeshift variant in NON repetitive region in NM_001128633.2.
BP6
Variant 22-21547775-A-ACACCTG is Benign according to our data. Variant chr22-21547775-A-ACACCTG is described in ClinVar as [Likely_benign]. Clinvar id is 1205884.Status of the report is no_assertion_criteria_provided, 0 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RIMBP3C | NM_001128633.2 | c.3201_3202insCAGGTG | p.Gln1066_Val1067dup | inframe_insertion | 1/1 | ENST00000433039.2 | NP_001122105.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RIMBP3C | ENST00000433039.2 | c.3201_3202insCAGGTG | p.Gln1066_Val1067dup | inframe_insertion | 1/1 | NM_001128633.2 | ENSP00000390630 | P1 |
Frequencies
GnomAD3 genomes AF: 0.409 AC: 134AN: 328Hom.: 62 Cov.: 0
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GnomAD3 exomes AF: 0.285 AC: 361AN: 1266Hom.: 177 AF XY: 0.274 AC XY: 172AN XY: 628
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.323 AC: 4065AN: 12584Hom.: 1955 Cov.: 0 AF XY: 0.279 AC XY: 2055AN XY: 7356
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GnomAD4 genome AF: 0.404 AC: 134AN: 332Hom.: 62 Cov.: 0 AF XY: 0.393 AC XY: 70AN XY: 178
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
not provided Benign:1
Likely benign, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at