rs200259378
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001128635.2(RIMBP3B):c.3919C>A(p.Pro1307Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 0)
Exomes 𝑓: 0.61 ( 10917 hom. )
Failed GnomAD Quality Control
Consequence
RIMBP3B
NM_001128635.2 missense
NM_001128635.2 missense
Scores
1
14
Clinical Significance
Conservation
PhyloP100: -1.47
Publications
2 publications found
Genes affected
RIMBP3B (HGNC:33891): (RIMS binding protein 3B) 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 was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.049946606).
BA1
GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.731 is higher than 0.05.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001128635.2. You can select a different transcript below to see updated ACMG assignments.
Frequencies
GnomAD3 genomes 0 Cov.: 0
GnomAD3 genomes
AC:
0
AN:
0
Hom.:
Cov.:
0
GnomAD4 exome AF: 0.610 AC: 43248AN: 70882Hom.: 10917 Cov.: 0 AF XY: 0.609 AC XY: 23424AN XY: 38486 show subpopulations
GnomAD4 exome
AF:
AC:
43248
AN:
70882
Hom.:
Cov.:
0
AF XY:
AC XY:
23424
AN XY:
38486
show subpopulations
African (AFR)
AF:
AC:
961
AN:
2552
American (AMR)
AF:
AC:
3069
AN:
4170
Ashkenazi Jewish (ASJ)
AF:
AC:
840
AN:
1344
East Asian (EAS)
AF:
AC:
4089
AN:
5448
South Asian (SAS)
AF:
AC:
8109
AN:
14252
European-Finnish (FIN)
AF:
AC:
1674
AN:
2560
Middle Eastern (MID)
AF:
AC:
131
AN:
216
European-Non Finnish (NFE)
AF:
AC:
22251
AN:
36882
Other (OTH)
AF:
AC:
2124
AN:
3458
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.548
Heterozygous variant carriers
0
534
1068
1601
2135
2669
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
296
592
888
1184
1480
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome 0 Cov.: 0AC XY: 0AN XY: 0
GnomAD4 genome
Data not reliable, filtered out with message: AC0;AS_VQSR
AC:
0
AN:
0
Hom.:
Cov.:
0
AC XY:
0
AN XY:
0
African (AFR)
AC:
0
AN:
0
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AC:
0
AN:
0
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AC:
0
AN:
0
Other (OTH)
AC:
0
AN:
0
Alfa
AF:
Hom.:
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
not specified (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
DANN
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
PhyloP100
PrimateAI
Benign
T
Sift4G
Uncertain
D
Vest4
MVP
ClinPred
T
GERP RS
Varity_R
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
Publications
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