rs2235015
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001348946.2(ABCB1):c.287-25G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 1,594,280 control chromosomes in the GnomAD database, including 31,840 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.22 ( 4369 hom., cov: 33)
Exomes 𝑓: 0.19 ( 27471 hom. )
Consequence
ABCB1
NM_001348946.2 intron
NM_001348946.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.26
Genes affected
ABCB1 (HGNC:40): (ATP binding cassette subfamily B member 1) The membrane-associated protein encoded by this gene is a member of 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 MDR/TAP subfamily. Members of the MDR/TAP subfamily are involved in multidrug resistance. The protein encoded by this gene is an ATP-dependent drug efflux pump for xenobiotic compounds with broad substrate specificity. It is responsible for decreased drug accumulation in multidrug-resistant cells and often mediates the development of resistance to anticancer drugs. This protein also functions as a transporter in the blood-brain barrier. Mutations in this gene are associated with colchicine resistance and Inflammatory bowel disease 13. Alternative splicing and the use of alternative promoters results in multiple transcript variants. [provided by RefSeq, Feb 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
?
Variant 7-87570248-C-A is Benign according to our data. Variant chr7-87570248-C-A is described in ClinVar as [Benign]. Clinvar id is 675797.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCB1 | NM_001348946.2 | c.287-25G>T | intron_variant | ENST00000622132.5 | |||
ABCB1 | NM_000927.5 | c.287-25G>T | intron_variant | ||||
ABCB1 | NM_001348944.2 | c.287-25G>T | intron_variant | ||||
ABCB1 | NM_001348945.2 | c.497-25G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCB1 | ENST00000622132.5 | c.287-25G>T | intron_variant | 1 | NM_001348946.2 | P1 | |||
ABCB1 | ENST00000265724.8 | c.287-25G>T | intron_variant | 1 | P1 | ||||
ABCB1 | ENST00000543898.5 | c.287-25G>T | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.224 AC: 34097AN: 151940Hom.: 4361 Cov.: 33
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GnomAD3 exomes AF: 0.178 AC: 44574AN: 250346Hom.: 4581 AF XY: 0.176 AC XY: 23812AN XY: 135404
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GnomAD4 exome AF: 0.189 AC: 273207AN: 1442222Hom.: 27471 Cov.: 28 AF XY: 0.188 AC XY: 135176AN XY: 718684
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GnomAD4 genome ? AF: 0.225 AC: 34154AN: 152058Hom.: 4369 Cov.: 33 AF XY: 0.221 AC XY: 16407AN XY: 74336
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ClinVar
Significance: Benign
Submissions summary: Benign:1Other:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 14, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Tramadol response Other:1
drug response, no assertion criteria provided | research | Bruce Budowle Laboratory, University of North Texas Health Science Center | Apr 28, 2018 | - T:M1 = postmortem ratio or tramadol to O-desmethyltramadol; t-MP = model-based clustered metabolizer phenotype inferred from T:M1 |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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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