7-27095697-A-ATGGTGGTGG
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate
The NM_005522.5(HOXA1):c.215_216insCCACCACCA(p.His70_His72dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000304 in 141,610 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00030 ( 0 hom., cov: 30)
Exomes 𝑓: 0.00067 ( 2 hom. )
Failed GnomAD Quality Control
Consequence
HOXA1
NM_005522.5 inframe_insertion
NM_005522.5 inframe_insertion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.59
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 Likely_benign. Variant got -2 ACMG points.
BP6
Variant 7-27095697-A-ATGGTGGTGG is Benign according to our data. Variant chr7-27095697-A-ATGGTGGTGG is described in ClinVar as [Likely_benign]. Clinvar id is 587896.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HOXA1 | NM_005522.5 | c.215_216insCCACCACCA | p.His70_His72dup | inframe_insertion | 1/2 | ENST00000643460.2 | NP_005513.2 | |
HOXA1 | NM_153620.3 | c.215_216insCCACCACCA | p.His70_His72dup | inframe_insertion | 1/3 | NP_705873.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HOXA1 | ENST00000643460.2 | c.215_216insCCACCACCA | p.His70_His72dup | inframe_insertion | 1/2 | NM_005522.5 | ENSP00000494260 | P1 | ||
HOXA1 | ENST00000355633.5 | c.215_216insCCACCACCA | p.His70_His72dup | inframe_insertion | 1/3 | 1 | ENSP00000347851 | |||
HOTAIRM1 | ENST00000495032.1 | n.26+41_26+49dup | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.000304 AC: 43AN: 141484Hom.: 0 Cov.: 30
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GnomAD3 exomes AF: 0.000818 AC: 190AN: 232380Hom.: 1 AF XY: 0.00117 AC XY: 147AN XY: 125726
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000668 AC: 540AN: 808064Hom.: 2 Cov.: 52 AF XY: 0.00102 AC XY: 395AN XY: 388578
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Data not reliable, filtered out with message: AS_VQSR
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GnomAD4 genome AF: 0.000304 AC: 43AN: 141610Hom.: 0 Cov.: 30 AF XY: 0.000448 AC XY: 31AN XY: 69196
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 30, 2017 | 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. - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at