GeneBe

rs552419485

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_030632.3(ASXL3):​c.-165_-133delGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000013 ( 0 hom., cov: 0)

Consequence

ASXL3
NM_030632.3 5_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.218

Publications

1 publications found
Variant links:
Genes affected
ASXL3 (HGNC:29357): (ASXL transcriptional regulator 3) This gene encodes a protein containing a plant homeodomain (PHD) zinc finger domain that plays a role in the regulation of gene transcription. The encoded protein has been shown to negatively regulate lipogenesis by binding to and inhibiting the transcriptional activity of two nuclear hormone receptors, oxysterols receptor LXR-alpha (LXRalpha) and thyroid hormone receptor beta (TRbeta). The encoded protein may also inhibit histone deubiquitination. Mutations in this gene have been identified in human patients with Bainbridge-Ropers syndrome, which is characterized by feeding difficulties, developmental delay and other features. [provided by RefSeq, May 2017]
ASXL3 Gene-Disease associations (from GenCC):
  • severe feeding difficulties-failure to thrive-microcephaly due to ASXL3 deficiency syndrome
    Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, G2P, Labcorp Genetics (formerly Invitae), Illumina
  • syndromic intellectual disability
    Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030632.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
ASXL3
NM_030632.3
MANE Select
c.-165_-133delGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCC
5_prime_UTR
Exon 1 of 12NP_085135.1Q9C0F0-1

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
ASXL3
ENST00000269197.12
TSL:5 MANE Select
c.-165_-133delGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCC
5_prime_UTR
Exon 1 of 12ENSP00000269197.4Q9C0F0-1
ASXL3
ENST00000696964.1
c.-165_-133delGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCC
5_prime_UTR
Exon 1 of 13ENSP00000513003.1A0A8V8TKV8
ASXL3
ENST00000681521.1
c.-165_-133delGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCC
5_prime_UTR
Exon 1 of 11ENSP00000506037.1A0A7P0TAE5

Frequencies

GnomAD3 genomes
AF:
0.0000134
AC:
1
AN:
74588
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.0000605
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0000134
AC:
1
AN:
74588
Hom.:
0
Cov.:
0
AF XY:
0.0000282
AC XY:
1
AN XY:
35418
show subpopulations
African (AFR)
AF:
0.0000605
AC:
1
AN:
16534
American (AMR)
AF:
0.00
AC:
0
AN:
8376
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
2220
East Asian (EAS)
AF:
0.00
AC:
0
AN:
2390
South Asian (SAS)
AF:
0.00
AC:
0
AN:
1854
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
2466
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
138
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
39320
Other (OTH)
AF:
0.00
AC:
0
AN:
916
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
0.00
Hom.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.22

Splicing

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

Publications

Other links and lift over

dbSNP: rs552419485; hg19: chr18-31158422; API