7-27095697-ATGG-A

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

Scores

Not classified

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 2.02
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]

Genome browser will be placed here

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

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
HOXA1NM_005522.5 linkc.213_215delCCA p.His72del disruptive_inframe_deletion 1/2 ENST00000643460.2 NP_005513.2 P49639
HOXA1NM_153620.3 linkc.213_215delCCA p.His72del disruptive_inframe_deletion 1/3 NP_705873.3 P49639

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
HOXA1ENST00000643460.2 linkc.213_215delCCA p.His72del disruptive_inframe_deletion 1/2 NM_005522.5 ENSP00000494260.2 A0A2R8Y4R9
HOXA1ENST00000355633.5 linkc.213_215delCCA p.His72del disruptive_inframe_deletion 1/31 ENSP00000347851.5 E7ERT8
HOTAIRM1ENST00000495032.1 linkn.26+47_26+49delTGG intron_variant 5

Frequencies

GnomAD3 genomes
AF:
0.00120
AC:
170
AN:
141466
Hom.:
0
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.00227
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00192
Gnomad ASJ
AF:
0.00127
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000940
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000639
Gnomad OTH
AF:
0.00207
GnomAD3 exomes
AF:
0.000783
AC:
182
AN:
232380
Hom.:
1
AF XY:
0.000803
AC XY:
101
AN XY:
125726
show subpopulations
Gnomad AFR exome
AF:
0.00263
Gnomad AMR exome
AF:
0.00111
Gnomad ASJ exome
AF:
0.000549
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000621
Gnomad FIN exome
AF:
0.000101
Gnomad NFE exome
AF:
0.000736
Gnomad OTH exome
AF:
0.000701
GnomAD4 exome
AF:
0.00110
AC:
885
AN:
801982
Hom.:
2
AF XY:
0.00118
AC XY:
454
AN XY:
385670
show subpopulations
Gnomad4 AFR exome
AF:
0.00235
Gnomad4 AMR exome
AF:
0.00331
Gnomad4 ASJ exome
AF:
0.000835
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00189
Gnomad4 FIN exome
AF:
0.000297
Gnomad4 NFE exome
AF:
0.00102
Gnomad4 OTH exome
AF:
0.00113
GnomAD4 genome
AF:
0.00121
AC:
171
AN:
141592
Hom.:
0
Cov.:
30
AF XY:
0.00129
AC XY:
89
AN XY:
69190
show subpopulations
Gnomad4 AFR
AF:
0.00226
Gnomad4 AMR
AF:
0.00192
Gnomad4 ASJ
AF:
0.00127
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000938
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000655
Gnomad4 OTH
AF:
0.00205
Bravo
AF:
0.00126

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 submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJun 08, 2018- -
Likely benign, criteria provided, single submitterclinical testingGeneDxMar 29, 2018This 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 submitterclinical testingGenetic Services Laboratory, University of ChicagoMar 13, 2019- -
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitterclinical testingAmbry GeneticsAug 25, 2018This 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

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs747464910; hg19: chr7-27135316; API