chr1-156381908-G-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_020407.5(RHBG):c.943G>A(p.Gly315Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.45 in 1,609,256 control chromosomes in the GnomAD database, including 165,875 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 0.48 ( 18171 hom., cov: 31)
Exomes 𝑓: 0.45 ( 147704 hom. )
Consequence
RHBG
NM_020407.5 missense
NM_020407.5 missense
Scores
5
4
3
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 7.76
Publications
28 publications found
Genes affected
RHBG (HGNC:14572): (Rh family B glycoprotein) This gene encodes one of two non-erythroid members of the Rhesus (Rh) protein family. Non-erythroid Rh protein family members are mainly expressed in the kidney and belong to the methylammonium-ammonium permease/ammonia transporters superfamily. All Rh family proteins are predicted to be transmembrane proteins with 12 membrane spanning domains and intracytoplasmic N- and C-termini. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jan 2012]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=3.0048128E-5).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.484 AC: 73532AN: 151772Hom.: 18168 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
73532
AN:
151772
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD2 exomes AF: 0.481 AC: 117936AN: 244952 AF XY: 0.470 show subpopulations
GnomAD2 exomes
AF:
AC:
117936
AN:
244952
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.446 AC: 650189AN: 1457366Hom.: 147704 Cov.: 50 AF XY: 0.445 AC XY: 322676AN XY: 725250 show subpopulations
GnomAD4 exome
AF:
AC:
650189
AN:
1457366
Hom.:
Cov.:
50
AF XY:
AC XY:
322676
AN XY:
725250
show subpopulations
African (AFR)
AF:
AC:
18045
AN:
33086
American (AMR)
AF:
AC:
25719
AN:
42608
Ashkenazi Jewish (ASJ)
AF:
AC:
11210
AN:
25900
East Asian (EAS)
AF:
AC:
27694
AN:
39680
South Asian (SAS)
AF:
AC:
37998
AN:
85766
European-Finnish (FIN)
AF:
AC:
22922
AN:
53386
Middle Eastern (MID)
AF:
AC:
2551
AN:
5754
European-Non Finnish (NFE)
AF:
AC:
476687
AN:
1110984
Other (OTH)
AF:
AC:
27363
AN:
60202
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.478
Heterozygous variant carriers
0
20212
40424
60636
80848
101060
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
14746
29492
44238
58984
73730
<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 AF: 0.484 AC: 73562AN: 151890Hom.: 18171 Cov.: 31 AF XY: 0.483 AC XY: 35821AN XY: 74212 show subpopulations
GnomAD4 genome
AF:
AC:
73562
AN:
151890
Hom.:
Cov.:
31
AF XY:
AC XY:
35821
AN XY:
74212
show subpopulations
African (AFR)
AF:
AC:
22356
AN:
41426
American (AMR)
AF:
AC:
8371
AN:
15254
Ashkenazi Jewish (ASJ)
AF:
AC:
1518
AN:
3472
East Asian (EAS)
AF:
AC:
3594
AN:
5152
South Asian (SAS)
AF:
AC:
2133
AN:
4810
European-Finnish (FIN)
AF:
AC:
4512
AN:
10534
Middle Eastern (MID)
AF:
AC:
131
AN:
290
European-Non Finnish (NFE)
AF:
AC:
29460
AN:
67942
Other (OTH)
AF:
AC:
988
AN:
2102
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1888
3776
5664
7552
9440
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
658
1316
1974
2632
3290
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
TwinsUK
AF:
AC:
1509
ALSPAC
AF:
AC:
1657
ESP6500AA
AF:
AC:
2175
ESP6500EA
AF:
AC:
3575
ExAC
AF:
AC:
57993
Asia WGS
AF:
AC:
1813
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Pathogenic
DANN
Pathogenic
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
MetaRNN
Benign
T
MetaSVM
Uncertain
T
PhyloP100
PrimateAI
Uncertain
T
REVEL
Uncertain
Sift4G
Pathogenic
D
Vest4
MutPred
Gain of methylation at G315 (P = 0.0123);
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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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