GeneBe

rs747464910

Variant names:

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_005522.5(HOXA1):​c.204_215delCCACCACCACCA​(p.His69_His72del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.00000248 in 808,074 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 30)
Exomes 𝑓: 0.0000025 ( 0 hom. )

Consequence

HOXA1
NM_005522.5 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.23
Variant links:
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 Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
HOXA1NM_005522.5 linkc.204_215delCCACCACCACCA p.His69_His72del disruptive_inframe_deletion Exon 1 of 2 ENST00000643460.2 NP_005513.2 P49639
HOXA1NM_153620.3 linkc.204_215delCCACCACCACCA p.His69_His72del disruptive_inframe_deletion Exon 1 of 3 NP_705873.3 P49639

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
HOXA1ENST00000643460.2 linkc.204_215delCCACCACCACCA p.His69_His72del disruptive_inframe_deletion Exon 1 of 2 NM_005522.5 ENSP00000494260.2 A0A2R8Y4R9
HOXA1ENST00000355633.5 linkc.204_215delCCACCACCACCA p.His69_His72del disruptive_inframe_deletion Exon 1 of 3 1 ENSP00000347851.5 E7ERT8
HOTAIRM1ENST00000495032.1 linkn.26+38_26+49delTGGTGGTGGTGG intron_variant Intron 1 of 1 5

Frequencies

GnomAD3 genomes
Cov.:
30
GnomAD4 exome
AF:
0.00000248
AC:
2
AN:
808074
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
388582
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.0000489
Gnomad4 NFE exome
AF:
0.00000152
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr7-27135316; API