22-21547630-C-G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_001128633.2(RIMBP3C):ā€‹c.3347G>Cā€‹(p.Gly1116Ala) variant causes a missense change involving the alteration of a conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (ā˜…).

Frequency

Genomes: š‘“ 0.011 ( 0 hom., cov: 0)
Exomes š‘“: 0.00099 ( 14 hom. )
Failed GnomAD Quality Control

Consequence

RIMBP3C
NM_001128633.2 missense

Scores

4
11
4

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 7.80
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
RIMBP3CNM_001128633.2 linkuse as main transcriptc.3347G>C p.Gly1116Ala missense_variant 1/1 ENST00000433039.2 NP_001122105.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
RIMBP3CENST00000433039.2 linkuse as main transcriptc.3347G>C p.Gly1116Ala missense_variant 1/1 NM_001128633.2 ENSP00000390630 P1

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
4
AN:
354
Hom.:
0
Cov.:
0
FAILED QC
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.0741
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.000993
AC:
82
AN:
82612
Hom.:
14
Cov.:
0
AF XY:
0.00118
AC XY:
52
AN XY:
44102
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00934
Gnomad4 SAS exome
AF:
0.000136
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00598
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.0112
AC:
4
AN:
356
Hom.:
0
Cov.:
0
AF XY:
0.0155
AC XY:
3
AN XY:
194
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.0741
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000422
Hom.:
0

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsMar 07, 2023The c.3347G>C (p.G1116A) alteration is located in exon 1 (coding exon 1) of the RIMBP3C gene. This alteration results from a G to C substitution at nucleotide position 3347, causing the glycine (G) at amino acid position 1116 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.50
BayesDel_addAF
Benign
-0.0024
T
BayesDel_noAF
Benign
-0.24
CADD
Pathogenic
27
DANN
Uncertain
1.0
DEOGEN2
Uncertain
0.74
.;D
Eigen
Uncertain
0.64
Eigen_PC
Uncertain
0.54
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Uncertain
0.88
D;D
M_CAP
Uncertain
0.18
D
MetaRNN
Uncertain
0.50
D;D
MetaSVM
Benign
-0.31
T
MutationAssessor
Pathogenic
3.0
.;M
MutationTaster
Benign
1.0
D;D
PrimateAI
Uncertain
0.79
T
PROVEAN
Pathogenic
-5.8
D;D
REVEL
Uncertain
0.39
Sift
Uncertain
0.015
D;D
Sift4G
Pathogenic
0.0
D;D
Vest4
0.63
MVP
0.42
ClinPred
0.99
D
GERP RS
3.3
Varity_R
0.61
gMVP
0.64

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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.

Other links and lift over

dbSNP: rs1305487013; hg19: chr22-21901919; API