chrX-75060016-TATA-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_001271696.3(ABCB7):c.2043+204_2043+206del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0283 in 112,029 control chromosomes in the GnomAD database, including 115 homozygotes. There are 750 hemizygotes in GnomAD. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.028 ( 115 hom., 750 hem., cov: 21)
Consequence
ABCB7
NM_001271696.3 intron
NM_001271696.3 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.09
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 -10 ACMG points.
BP6
?
Variant X-75060016-TATA-T is Benign according to our data. Variant chrX-75060016-TATA-T is described in ClinVar as [Benign]. Clinvar id is 1292863.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0958 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCB7 | NM_001271696.3 | c.2043+204_2043+206del | intron_variant | ENST00000373394.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCB7 | ENST00000373394.8 | c.2043+204_2043+206del | intron_variant | 1 | NM_001271696.3 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0283 AC: 3168AN: 111979Hom.: 115 Cov.: 21 AF XY: 0.0219 AC XY: 749AN XY: 34167
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GnomAD4 genome ? AF: 0.0283 AC: 3171AN: 112029Hom.: 115 Cov.: 21 AF XY: 0.0219 AC XY: 750AN XY: 34227
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 31, 2018 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at