rs387906869
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_004827.3(ABCG2):c.1111_1112delAC(p.Thr371LeufsTer20) variant causes a frameshift change. The variant allele was found at a frequency of 0.00000342 in 1,461,874 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: 0.0000034 ( 0 hom. )
Consequence
ABCG2
NM_004827.3 frameshift
NM_004827.3 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 5.86
Publications
4 publications found
Genes affected
ABCG2 (HGNC:74): (ATP binding cassette subfamily G member 2 (JR blood group)) The membrane-associated protein encoded by this gene is included in the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intra-cellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). This protein is a member of the White subfamily. Alternatively referred to as a breast cancer resistance protein, this protein functions as a xenobiotic transporter which may play a major role in multi-drug resistance. It likely serves as a cellular defense mechanism in response to mitoxantrone and anthracycline exposure. Significant expression of this protein has been observed in the placenta, which may suggest a potential role for this molecule in placenta tissue. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2012]
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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_004827.3. 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 |
|---|---|---|---|---|---|---|---|---|---|
| ABCG2 | NM_004827.3 | MANE Select | c.1111_1112delAC | p.Thr371LeufsTer20 | frameshift | Exon 9 of 16 | NP_004818.2 | ||
| ABCG2 | NM_001348985.1 | c.1111_1112delAC | p.Thr371LeufsTer20 | frameshift | Exon 10 of 17 | NP_001335914.1 | |||
| ABCG2 | NM_001348986.2 | c.1111_1112delAC | p.Thr371LeufsTer20 | frameshift | Exon 9 of 16 | NP_001335915.1 |
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| ABCG2 | ENST00000237612.8 | TSL:1 MANE Select | c.1111_1112delAC | p.Thr371LeufsTer20 | frameshift | Exon 9 of 16 | ENSP00000237612.3 | ||
| ABCG2 | ENST00000515655.5 | TSL:1 | c.1111_1112delAC | p.Thr371LeufsTer20 | frameshift | Exon 9 of 16 | ENSP00000426917.1 | ||
| ABCG2 | ENST00000650821.1 | c.1111_1112delAC | p.Thr371LeufsTer20 | frameshift | Exon 10 of 17 | ENSP00000498246.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD2 exomes AF: 0.00000796 AC: 2AN: 251380 AF XY: 0.00000736 show subpopulations
GnomAD2 exomes
AF:
AC:
2
AN:
251380
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: 0.00000342 AC: 5AN: 1461874Hom.: 0 AF XY: 0.00000413 AC XY: 3AN XY: 727238 show subpopulations
GnomAD4 exome
AF:
AC:
5
AN:
1461874
Hom.:
AF XY:
AC XY:
3
AN XY:
727238
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33480
American (AMR)
AF:
AC:
0
AN:
44724
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26134
East Asian (EAS)
AF:
AC:
0
AN:
39698
South Asian (SAS)
AF:
AC:
5
AN:
86258
European-Finnish (FIN)
AF:
AC:
0
AN:
53420
Middle Eastern (MID)
AF:
AC:
0
AN:
5768
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1111996
Other (OTH)
AF:
AC:
0
AN:
60396
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.425
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
ClinVar submissions as Germline
Significance:Affects
Revision:no assertion criteria provided
Pathogenic
VUS
Benign
Condition
-
-
-
BLOOD GROUP, JUNIOR SYSTEM (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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