rs387906265
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 3 ACMG points: 3P and 0B. PM2PP5
The NM_001017922.2(ERMAP):c.307_308delGA(p.Asp103CysfsTer12) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,132 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Consequence
ERMAP
NM_001017922.2 frameshift
NM_001017922.2 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 3.25
Publications
1 publications found
Genes affected
ERMAP (HGNC:15743): (erythroblast membrane associated protein (Scianna blood group)) The protein encoded by this gene is a cell surface transmembrane protein that may act as an erythroid cell receptor, possibly as a mediator of cell adhesion. Polymorphisms in this gene are responsible for the Scianna/Radin blood group system. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 1-42830984-TGA-T is Pathogenic according to our data. Variant chr1-42830984-TGA-T is described in ClinVar as Pathogenic. ClinVar VariationId is 1915.Status of the report is no_assertion_criteria_provided, 0 stars.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001017922.2. 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 |
|---|---|---|---|---|---|---|---|---|---|
| ERMAP | NM_001017922.2 | MANE Select | c.307_308delGA | p.Asp103CysfsTer12 | frameshift | Exon 4 of 12 | NP_001017922.1 | ||
| ERMAP | NM_018538.4 | c.307_308delGA | p.Asp103CysfsTer12 | frameshift | Exon 3 of 11 | NP_061008.2 |
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| ERMAP | ENST00000372517.8 | TSL:1 MANE Select | c.307_308delGA | p.Asp103CysfsTer12 | frameshift | Exon 4 of 12 | ENSP00000361595.2 | ||
| ERMAP | ENST00000372514.7 | TSL:1 | c.307_308delGA | p.Asp103CysfsTer12 | frameshift | Exon 3 of 11 | ENSP00000361592.3 | ||
| ERMAP | ENST00000328249.3 | TSL:1 | n.1075_1076delGA | non_coding_transcript_exon | Exon 1 of 9 |
Frequencies
GnomAD3 genomes 0.00000657 AC: 1AN: 152132Hom.: 0 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
152132
Hom.:
Cov.:
32
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome 0.00000657 AC: 1AN: 152132Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74334 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
152132
Hom.:
Cov.:
32
AF XY:
AC XY:
0
AN XY:
74334
show subpopulations
African (AFR)
AF:
AC:
1
AN:
41428
American (AMR)
AF:
AC:
0
AN:
15276
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3470
East Asian (EAS)
AF:
AC:
0
AN:
5188
South Asian (SAS)
AF:
AC:
0
AN:
4828
European-Finnish (FIN)
AF:
AC:
0
AN:
10618
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
0
AN:
68002
Other (OTH)
AF:
AC:
0
AN:
2094
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
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.:
Bravo
AF:
ClinVar
ClinVar submissions as Germline
Significance:Pathogenic
Revision:no assertion criteria provided
Pathogenic
VUS
Benign
Condition
1
-
-
SCIANNA BLOOD GROUP SYSTEM, SC:-1,-2 (1)
Computational 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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