NM_003226.4:c.83-190C>T
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003226.4(TFF3):c.83-190C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.423 in 611,458 control chromosomes in the GnomAD database, including 56,884 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.41 ( 13405 hom., cov: 32)
Exomes 𝑓: 0.43 ( 43479 hom. )
Consequence
TFF3
NM_003226.4 intron
NM_003226.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.940
Publications
2 publications found
Genes affected
TFF3 (HGNC:11757): (trefoil factor 3) Members of the trefoil family are characterized by having at least one copy of the trefoil motif, a 40-amino acid domain that contains three conserved disulfides. They are stable secretory proteins expressed in gastrointestinal mucosa. Their functions are not defined, but they may protect the mucosa from insults, stabilize the mucus layer and affect healing of the epithelium. This gene is expressed in goblet cells of the intestines and colon. This gene and two other related trefoil family member genes are found in a cluster on chromosome 21. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TFF3 | ENST00000518498.3 | c.83-190C>T | intron_variant | Intron 1 of 2 | 1 | NM_003226.4 | ENSP00000430690.2 | |||
TFF3 | ENST00000398431.2 | c.44-146C>T | intron_variant | Intron 1 of 2 | 3 | ENSP00000381462.2 | ||||
TFF3 | ENST00000489676.1 | n.-135C>T | upstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.415 AC: 62993AN: 151884Hom.: 13395 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
62993
AN:
151884
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.426 AC: 195867AN: 459456Hom.: 43479 AF XY: 0.424 AC XY: 100876AN XY: 237736 show subpopulations
GnomAD4 exome
AF:
AC:
195867
AN:
459456
Hom.:
AF XY:
AC XY:
100876
AN XY:
237736
show subpopulations
African (AFR)
AF:
AC:
4027
AN:
10410
American (AMR)
AF:
AC:
4409
AN:
10756
Ashkenazi Jewish (ASJ)
AF:
AC:
5565
AN:
12754
East Asian (EAS)
AF:
AC:
5234
AN:
24552
South Asian (SAS)
AF:
AC:
14466
AN:
38230
European-Finnish (FIN)
AF:
AC:
10764
AN:
28034
Middle Eastern (MID)
AF:
AC:
794
AN:
1972
European-Non Finnish (NFE)
AF:
AC:
139856
AN:
307094
Other (OTH)
AF:
AC:
10752
AN:
25654
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.506
Heterozygous variant carriers
0
5171
10343
15514
20686
25857
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
1598
3196
4794
6392
7990
<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 AF: 0.415 AC: 63047AN: 152002Hom.: 13405 Cov.: 32 AF XY: 0.408 AC XY: 30311AN XY: 74310 show subpopulations
GnomAD4 genome
AF:
AC:
63047
AN:
152002
Hom.:
Cov.:
32
AF XY:
AC XY:
30311
AN XY:
74310
show subpopulations
African (AFR)
AF:
AC:
15821
AN:
41442
American (AMR)
AF:
AC:
6338
AN:
15292
Ashkenazi Jewish (ASJ)
AF:
AC:
1524
AN:
3466
East Asian (EAS)
AF:
AC:
921
AN:
5166
South Asian (SAS)
AF:
AC:
1811
AN:
4806
European-Finnish (FIN)
AF:
AC:
3935
AN:
10584
Middle Eastern (MID)
AF:
AC:
98
AN:
292
European-Non Finnish (NFE)
AF:
AC:
31209
AN:
67932
Other (OTH)
AF:
AC:
856
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.498
Heterozygous variant carriers
0
1846
3693
5539
7386
9232
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
592
1184
1776
2368
2960
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
902
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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