rs387906908
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2
The NM_005689.4(ABCB6):c.1690_1691delAT(p.Met564ValfsTer2) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000752 in 1,461,890 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Affects (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000075 ( 0 hom. )
Consequence
ABCB6
NM_005689.4 frameshift
NM_005689.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 9.18
Publications
5 publications found
Genes affected
ABCB6 (HGNC:47): (ATP binding cassette subfamily B member 6 (LAN blood group)) This gene encodes a member of the ATP-binding cassette (ABC) transporter superfamily. ABC proteins transport various molecules across extra- and intra-cellular membranes. This protein is a member of the heavy metal importer subfamily and plays a role in porphyrin transport. This gene is the molecular basis of the Langereis (Lan) blood group antigen and mutations in this gene underlie familial pseudohyperkalemia and dyschromatosis universalis hereditaria. [provided by RefSeq, Mar 2017]
ABCB6 Gene-Disease associations (from GenCC):
- dyschromatosis universalis hereditaria 3Inheritance: AD Classification: STRONG, LIMITED Submitted by: G2P, Labcorp Genetics (formerly Invitae)
- dyschromatosis universalis hereditariaInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- familial pseudohyperkalemiaInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- microphthalmia, isolated, with colobomaInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- microphthalmia, isolated, with coloboma 7Inheritance: AD Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae), PanelApp Australia, G2P
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -4 ACMG points.
BS2
High AC in GnomAdExome4 at 11 AD gene.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_005689.4. 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 |
|---|---|---|---|---|---|---|---|---|---|
| ABCB6 | NM_005689.4 | MANE Select | c.1690_1691delAT | p.Met564ValfsTer2 | frameshift | Exon 11 of 19 | NP_005680.1 | ||
| ABCB6 | NM_001349828.2 | c.1552_1553delAT | p.Met518ValfsTer2 | frameshift | Exon 10 of 18 | NP_001336757.1 |
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| ABCB6 | ENST00000265316.9 | TSL:1 MANE Select | c.1690_1691delAT | p.Met564ValfsTer2 | frameshift | Exon 11 of 19 | ENSP00000265316.3 | ||
| ENSG00000284820 | ENST00000446716.5 | TSL:2 | n.*3649_*3650delAT | non_coding_transcript_exon | Exon 15 of 22 | ENSP00000398528.1 | |||
| ENSG00000284820 | ENST00000446716.5 | TSL:2 | n.*3649_*3650delAT | 3_prime_UTR | Exon 15 of 22 | ENSP00000398528.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000752 AC: 11AN: 1461890Hom.: 0 AF XY: 0.00000825 AC XY: 6AN XY: 727246 show subpopulations
GnomAD4 exome
AF:
AC:
11
AN:
1461890
Hom.:
AF XY:
AC XY:
6
AN XY:
727246
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33480
American (AMR)
AF:
AC:
0
AN:
44724
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26136
East Asian (EAS)
AF:
AC:
1
AN:
39700
South Asian (SAS)
AF:
AC:
9
AN:
86258
European-Finnish (FIN)
AF:
AC:
0
AN:
53416
Middle Eastern (MID)
AF:
AC:
0
AN:
5768
European-Non Finnish (NFE)
AF:
AC:
1
AN:
1112012
Other (OTH)
AF:
AC:
0
AN:
60396
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.484
Heterozygous variant carriers
0
1
2
3
4
5
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
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>80
Age
GnomAD4 genome
GnomAD4 genome
Cov.:
32
Alfa
AF:
Hom.:
ClinVar
ClinVar submissions as Germline
Significance:Affects
Revision:no assertion criteria provided
Pathogenic
VUS
Benign
Condition
-
-
-
Langereis blood group (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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