6-49607201-CT-C
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Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_000324.3(RHAG):c.1086del(p.Ala363LeufsTer15) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 33)
Consequence
RHAG
NM_000324.3 frameshift
NM_000324.3 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.249
Genes affected
RHAG (HGNC:10006): (Rh associated glycoprotein) The protein encoded by this gene is erythrocyte-specific and is thought to be part of a membrane channel that transports ammonium and carbon dioxide across the blood cell membrane. The encoded protein appears to interact with Rh blood group antigens and Rh30 polypeptides. Defects in this gene are a cause of regulator type Rh-null hemolytic anemia (RHN), or Rh-deficiency syndrome.[provided by RefSeq, Mar 2009]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 11 ACMG points.
PVS1
?
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 6-49607201-CT-C is Pathogenic according to our data. Variant chr6-49607201-CT-C is described in ClinVar as [Pathogenic]. Clinvar id is 13058.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RHAG | NM_000324.3 | c.1086del | p.Ala363LeufsTer15 | frameshift_variant | 8/10 | ENST00000371175.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RHAG | ENST00000371175.10 | c.1086del | p.Ala363LeufsTer15 | frameshift_variant | 8/10 | 1 | NM_000324.3 | P2 | |
RHAG | ENST00000646272.1 | c.1086del | p.Ala363LeufsTer15 | frameshift_variant | 8/10 | A2 | |||
RHAG | ENST00000646963.1 | c.1086del | p.Ala363LeufsTer15 | frameshift_variant | 8/9 | ||||
RHAG | ENST00000646939.1 | c.964del | p.Ser322AlafsTer48 | frameshift_variant | 7/9 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
GnomAD4 exome Cov.: 30
GnomAD4 exome
Cov.:
30
GnomAD4 genome ? Cov.: 33
GnomAD4 genome
?
Cov.:
33
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Rh-null, regulator type Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Feb 01, 1996 | - - |
Computational scores
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Calibrated prediction
Score
Prediction
Splicing
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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