chrX-75060206-A-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001271696.3(ABCB7):c.2043+17T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0159 in 1,157,106 control chromosomes in the GnomAD database, including 1,813 homozygotes. There are 4,876 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.081 ( 925 hom., 2439 hem., cov: 22)
Exomes 𝑓: 0.0090 ( 888 hom. 2437 hem. )
Consequence
ABCB7
NM_001271696.3 intron
NM_001271696.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.828
Genes affected
ABCB7 (HGNC:48): (ATP binding cassette subfamily B member 7) 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 as well as antigen presentation. This gene encodes a half-transporter involved in the transport of heme from the mitochondria to the cytosol. With iron/sulfur cluster precursors as its substrates, this protein may play a role in metal homeostasis. Mutations in this gene have been associated with mitochondrial iron accumulation and isodicentric (X)(q13) and sideroblastic anemia. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Nov 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.6).
BP6
?
Variant X-75060206-A-T is Benign according to our data. Variant chrX-75060206-A-T is described in ClinVar as [Benign]. Clinvar id is 136247.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.276 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCB7 | NM_001271696.3 | c.2043+17T>A | intron_variant | ENST00000373394.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCB7 | ENST00000373394.8 | c.2043+17T>A | intron_variant | 1 | NM_001271696.3 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0813 AC: 9067AN: 111532Hom.: 922 Cov.: 22 AF XY: 0.0721 AC XY: 2432AN XY: 33724
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GnomAD3 exomes AF: 0.0239 AC: 4307AN: 179854Hom.: 442 AF XY: 0.0154 AC XY: 998AN XY: 64754
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GnomAD4 exome AF: 0.00897 AC: 9378AN: 1045523Hom.: 888 Cov.: 22 AF XY: 0.00756 AC XY: 2437AN XY: 322309
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GnomAD4 genome ? AF: 0.0813 AC: 9075AN: 111583Hom.: 925 Cov.: 22 AF XY: 0.0722 AC XY: 2439AN XY: 33785
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 24, 2012 | 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. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
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Name
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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