Variant chr22-21547775-A-ACACCTG details in Genebe, Genetics Data Aggregator

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

Scores

Not classified

Clinical Significance

Benign/Likely benign no assertion criteria provided B:2

Conservation

PhyloP100: -0.0600

Variant links:

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]

RIMBP3C links:

Genome browser will be placed here

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 linkuse as main transcript	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 linkuse as main transcript	c.3201_3202insCAGGTG	p.Gln1066_Val1067dup	inframe_insertion	1/1		NM_001128633.2	ENSP00000390630	P1

Frequencies

GnomAD3 genomes

AF:

0.409

AC:

134

AN:

328

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.333

Gnomad AMI

AF:

0.667

Gnomad AMR

AF:

0.160

Gnomad ASJ

AF:

1.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.192

Gnomad FIN

AF:

1.00

Gnomad NFE

AF:

0.880

Gnomad OTH

AF:

0.400

GnomAD3 exomes

AF:

0.285

AC:

361

AN:

1266

Hom.:

177

AF XY:

0.274

AC XY:

172

AN XY:

628

show subpopulations

Gnomad AFR exome

AF:

0.567

Gnomad AMR exome

AF:

0.371

Gnomad ASJ exome

AF:

1.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0545

Gnomad FIN exome

AF:

0.882

Gnomad NFE exome

AF:

0.906

Gnomad OTH exome

AF:

0.263

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.323

AC:

4065

AN:

12584

Hom.:

1955

Cov.:

AF XY:

0.279

AC XY:

2055

AN XY:

7356

show subpopulations

Gnomad4 AFR exome

AF:

0.470

Gnomad4 AMR exome

AF:

0.417

Gnomad4 ASJ exome

AF:

0.971

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0794

Gnomad4 FIN exome

AF:

0.655

Gnomad4 NFE exome

AF:

0.804

Gnomad4 OTH exome

AF:

0.284

GnomAD4 genome

AF:

0.404

AC:

134

AN:

332

Hom.:

Cov.:

AF XY:

0.393

AC XY:

AN XY:

178

show subpopulations

Gnomad4 AFR

AF:

0.333

Gnomad4 AMR

AF:

0.160

Gnomad4 ASJ

AF:

1.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.185

Gnomad4 FIN

AF:

1.00

Gnomad4 NFE

AF:

0.880

Gnomad4 OTH

AF:

0.333

Alfa

AF:

0.364

Hom.:

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

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over