rs11303415
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_020407.5(RHBG):c.1271delC(p.Pro424GlnfsTer26) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000316 in 1,584,714 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0000028 ( 0 hom. )
Consequence
RHBG
NM_020407.5 frameshift
NM_020407.5 frameshift
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.618
Publications
17 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: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_020407.5. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| RHBG | NM_020407.5 | MANE Select | c.1271delC | p.Pro424GlnfsTer26 | frameshift | Exon 9 of 10 | NP_065140.3 | ||
| RHBG | NM_001256396.2 | c.1181delC | p.Pro394GlnfsTer26 | frameshift | Exon 10 of 11 | NP_001243325.1 | |||
| RHBG | NM_001256395.2 | c.1064delC | p.Pro355GlnfsTer26 | frameshift | Exon 10 of 11 | NP_001243324.1 |
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| RHBG | ENST00000537040.6 | TSL:1 MANE Select | c.1271delC | p.Pro424GlnfsTer26 | frameshift | Exon 9 of 10 | ENSP00000441197.2 | ||
| RHBG | ENST00000612897.4 | TSL:1 | n.*882delC | non_coding_transcript_exon | Exon 10 of 11 | ENSP00000477836.1 | |||
| RHBG | ENST00000613460.4 | TSL:1 | n.*1100delC | non_coding_transcript_exon | Exon 10 of 11 | ENSP00000483178.1 |
Frequencies
GnomAD3 genomes 0.00000660 AC: 1AN: 151624Hom.: 0 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
151624
Hom.:
Cov.:
0
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:
GnomAD4 exome AF: 0.00000279 AC: 4AN: 1433090Hom.: 0 Cov.: 46 AF XY: 0.00000141 AC XY: 1AN XY: 710776 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
4
AN:
1433090
Hom.:
Cov.:
46
AF XY:
AC XY:
1
AN XY:
710776
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
1
AN:
32754
American (AMR)
AF:
AC:
0
AN:
41788
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
24424
East Asian (EAS)
AF:
AC:
0
AN:
39280
South Asian (SAS)
AF:
AC:
0
AN:
82964
European-Finnish (FIN)
AF:
AC:
0
AN:
52446
Middle Eastern (MID)
AF:
AC:
0
AN:
5622
European-Non Finnish (NFE)
AF:
AC:
3
AN:
1094676
Other (OTH)
AF:
AC:
0
AN:
59136
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.00667379), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.313
Heterozygous variant carriers
0
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2
2
3
4
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0.20
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0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
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Age
GnomAD4 genome 0.00000660 AC: 1AN: 151624Hom.: 0 Cov.: 0 AF XY: 0.0000135 AC XY: 1AN XY: 73992 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
151624
Hom.:
Cov.:
0
AF XY:
AC XY:
1
AN XY:
73992
show subpopulations
African (AFR)
AF:
AC:
1
AN:
41216
American (AMR)
AF:
AC:
0
AN:
15220
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3470
East Asian (EAS)
AF:
AC:
0
AN:
5142
South Asian (SAS)
AF:
AC:
0
AN:
4794
European-Finnish (FIN)
AF:
AC:
0
AN:
10552
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
0
AN:
67920
Other (OTH)
AF:
AC:
0
AN:
2084
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
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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