GeneBe

NM_001081550.2:c.769-16_769-11delTTTTTT

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001081550.2(THOC2):​c.769-16_769-11delTTTTTT variant causes a intron change. The variant allele was found at a frequency of 0.00000108 in 924,015 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 23)
Exomes 𝑓: 0.0000011 ( 0 hom. 0 hem. )

Consequence

THOC2
NM_001081550.2 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.24

Publications

0 publications found
Variant links:
Genes affected
THOC2 (HGNC:19073): (THO complex subunit 2) The TREX multiprotein complex binds specifically to spliced mRNAs to facilitate mRNA export. The protein encoded by this gene is a member of the THO complex, a subset of the TREX complex. The encoded protein interacts with the THOC1 protein.[provided by RefSeq, Jun 2010]
THOC2 Gene-Disease associations (from GenCC):
  • X-linked intellectual disability-short stature-overweight syndrome
    Inheritance: XL Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: G2P, Labcorp Genetics (formerly Invitae), Orphanet, Ambry Genetics

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 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
THOC2NM_001081550.2 linkc.769-16_769-11delTTTTTT intron_variant Intron 8 of 38 ENST00000245838.13 NP_001075019.1 Q8NI27-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
THOC2ENST00000245838.13 linkc.769-16_769-11delTTTTTT intron_variant Intron 8 of 38 5 NM_001081550.2 ENSP00000245838.8 Q8NI27-1
THOC2ENST00000355725.8 linkc.769-16_769-11delTTTTTT intron_variant Intron 8 of 38 5 ENSP00000347959.4 Q8NI27-1
THOC2ENST00000491737.5 linkc.424-16_424-11delTTTTTT intron_variant Intron 4 of 33 5 ENSP00000419795.1 A0A0C4DG98
THOC2ENST00000433883.1 linkn.*399-16_*399-11delTTTTTT intron_variant Intron 8 of 9 5 ENSP00000415374.1 F2Z2V2

Frequencies

GnomAD3 genomes
Cov.:
23
GnomAD4 exome
AF:
0.00000108
AC:
1
AN:
924015
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
271363
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
21432
American (AMR)
AF:
0.00
AC:
0
AN:
25414
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
15629
East Asian (EAS)
AF:
0.00
AC:
0
AN:
25894
South Asian (SAS)
AF:
0.00
AC:
0
AN:
39605
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
35968
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
3353
European-Non Finnish (NFE)
AF:
0.00000139
AC:
1
AN:
718099
Other (OTH)
AF:
0.00
AC:
0
AN:
38621
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.575
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
Cov.:
23

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
6.2

Splicing

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

Publications

Other links and lift over

dbSNP: rs201356571; hg19: chrX-122805622; API