7-27095697-ATGG-A
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP6_Very_StrongBS2
The NM_005522.5(HOXA1):c.213_215delCCA(p.His72del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00112 in 943,574 control chromosomes in the GnomAD database, including 2 homozygotes. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. H71H) has been classified as Benign.
Frequency
Genomes: 𝑓 0.0012 ( 0 hom., cov: 30)
Exomes 𝑓: 0.0011 ( 2 hom. )
Consequence
HOXA1
NM_005522.5 disruptive_inframe_deletion
NM_005522.5 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.02
Genes affected
HOXA1 (HGNC:5099): (homeobox A1) In vertebrates, the genes encoding the class of transcription factors called homeobox genes are found in clusters named A, B, C, and D on four separate chromosomes. Expression of these proteins is spatially and temporally regulated during embryonic development. This gene is part of the A cluster on chromosome 7 and encodes a DNA-binding transcription factor which may regulate gene expression, morphogenesis, and differentiation. The encoded protein may be involved in the placement of hindbrain segments in the proper location along the anterior-posterior axis during development. Two transcript variants encoding two different isoforms have been found for this gene, with only one of the isoforms containing the homeodomain region. [provided by RefSeq, Jul 2008]
HOTAIRM1 (HGNC:37117): (HOXA transcript antisense RNA, myeloid-specific 1) This non-coding locus is located in the HOX gene cluster. Transcription of this locus is induced by retinoic acid, and transcripts likely function in regulation of myelopoiesis through transcriptional activation of several genes in the HOXA cluster, in addition to several beta-2 integrins. [provided by RefSeq, Jan 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP6
Variant 7-27095697-ATGG-A is Benign according to our data. Variant chr7-27095697-ATGG-A is described in ClinVar as [Likely_benign]. Clinvar id is 588087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-27095697-ATGG-A is described in Lovd as [Likely_benign].
BS2
High Homozygotes in GnomAdExome4 at 2 AR gene
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HOXA1 | ENST00000643460.2 | c.213_215delCCA | p.His72del | disruptive_inframe_deletion | 1/2 | NM_005522.5 | ENSP00000494260.2 | |||
HOXA1 | ENST00000355633.5 | c.213_215delCCA | p.His72del | disruptive_inframe_deletion | 1/3 | 1 | ENSP00000347851.5 | |||
HOTAIRM1 | ENST00000495032.1 | n.26+47_26+49delTGG | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00120 AC: 170AN: 141466Hom.: 0 Cov.: 30
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GnomAD3 exomes AF: 0.000783 AC: 182AN: 232380Hom.: 1 AF XY: 0.000803 AC XY: 101AN XY: 125726
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GnomAD4 exome AF: 0.00110 AC: 885AN: 801982Hom.: 2 AF XY: 0.00118 AC XY: 454AN XY: 385670
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GnomAD4 genome AF: 0.00121 AC: 171AN: 141592Hom.: 0 Cov.: 30 AF XY: 0.00129 AC XY: 89AN XY: 69190
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ClinVar
Significance: Likely benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jun 08, 2018 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 29, 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. - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Mar 13, 2019 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 25, 2018 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at