GeneBe

rs55725917

Variant names:

Variant summary

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

The NM_001083962.2(TCF4):​c.72+829_73-802delGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCT variant causes a intron 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 0.000022 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

TCF4
NM_001083962.2 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.885

Publications

0 publications found
Variant links:
Genes affected
TCF4 (HGNC:11634): (transcription factor 4) This gene encodes transcription factor 4, a basic helix-loop-helix transcription factor. The encoded protein recognizes an Ephrussi-box ('E-box') binding site ('CANNTG') - a motif first identified in immunoglobulin enhancers. This gene is broadly expressed, and may play an important role in nervous system development. Defects in this gene are a cause of Pitt-Hopkins syndrome. In addition, an intronic CTG repeat normally numbering 10-37 repeat units can expand to >50 repeat units and cause Fuchs endothelial corneal dystrophy. Multiple alternatively spliced transcript variants that encode different proteins have been described. [provided by RefSeq, Jul 2016]
TCF4 Gene-Disease associations (from GenCC):
  • Pitt-Hopkins syndrome
    Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, PanelApp Australia, Orphanet, Ambry Genetics, ClinGen, Labcorp Genetics (formerly Invitae)
  • corneal dystrophy, Fuchs endothelial, 3
    Inheritance: AD Classification: STRONG Submitted by: G2P
  • autosomal dominant non-syndromic intellectual disability
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
  • Fuchs' endothelial dystrophy
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
  • autism spectrum disorder
    Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
  • intellectual disability
    Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

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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_001083962.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
TCF4
NM_001083962.2
MANE Select
c.72+829_73-802delGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCT
intron
N/ANP_001077431.1P15884-3
TCF4
NM_001243226.3
c.378+829_379-802delGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCT
intron
N/ANP_001230155.2E9PH57
TCF4
NM_001243228.2
c.72+829_73-802delGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCT
intron
N/ANP_001230157.1H3BTP3

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
TCF4
ENST00000354452.8
TSL:5 MANE Select
c.72+829_73-802delGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCT
intron
N/AENSP00000346440.3P15884-3
TCF4
ENST00000398339.5
TSL:1
c.378+829_379-802delGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCT
intron
N/AENSP00000381382.1E9PH57
TCF4
ENST00000356073.8
TSL:1
c.72+829_73-802delGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCT
intron
N/AENSP00000348374.4P15884-1

Frequencies

GnomAD3 genomes
AF:
0.0000221
AC:
3
AN:
135448
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.0000266
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:
0.0000326
Gnomad OTH
AF:
0.00
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
0.00
AC:
0
AN:
572600
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
299152
African (AFR)
AF:
0.00
AC:
0
AN:
18026
American (AMR)
AF:
0.00
AC:
0
AN:
22006
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
14912
East Asian (EAS)
AF:
0.00
AC:
0
AN:
24090
South Asian (SAS)
AF:
0.00
AC:
0
AN:
53224
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
23366
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
2436
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
386774
Other (OTH)
AF:
0.00
AC:
0
AN:
27766
GnomAD4 genome
AF:
0.0000221
AC:
3
AN:
135448
Hom.:
0
Cov.:
0
AF XY:
0.0000306
AC XY:
2
AN XY:
65446
show subpopulations
African (AFR)
AF:
0.0000266
AC:
1
AN:
37558
American (AMR)
AF:
0.00
AC:
0
AN:
12930
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3176
East Asian (EAS)
AF:
0.00
AC:
0
AN:
4392
South Asian (SAS)
AF:
0.00
AC:
0
AN:
3990
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
9126
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
304
European-Non Finnish (NFE)
AF:
0.0000326
AC:
2
AN:
61278
Other (OTH)
AF:
0.00
AC:
0
AN:
1856
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.442
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome 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

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.89

Splicing

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

Publications

Other links and lift over

dbSNP: rs55725917; hg19: chr18-53253384; API