rs387906869
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_004827.3(ABCG2):c.1111_1112delAC(p.Thr371fs) 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
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 made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| ABCG2 | NM_004827.3 | c.1111_1112delAC | p.Thr371fs | frameshift_variant | 9/16 | ENST00000237612.8 | NP_004818.2 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| ABCG2 | ENST00000237612.8 | c.1111_1112delAC | p.Thr371fs | frameshift_variant | 9/16 | 1 | NM_004827.3 | ENSP00000237612.3 | ||
| ABCG2 | ENST00000515655.5 | c.1111_1112delAC | p.Thr371fs | frameshift_variant | 9/16 | 1 | ENSP00000426917.1 | |||
| ABCG2 | ENST00000650821.1 | c.1111_1112delAC | p.Thr371fs | frameshift_variant | 10/17 | ENSP00000498246.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251380Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135856
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GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461874Hom.: 0 AF XY: 0.00000413 AC XY: 3AN XY: 727238
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GnomAD4 genome
GnomAD4 genome
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32
ClinVar
Significance: Affects
Submissions summary: Other:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
BLOOD GROUP, JUNIOR SYSTEM Other:1
| Affects, no assertion criteria provided | literature only | OMIM | Jan 15, 2012 | - - |
Computational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at