rs11701143
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The variant allele was found at a frequency of 0.0328 in 1,614,134 control chromosomes in the GnomAD database, including 1,227 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 0.052 ( 325 hom., cov: 32)
Exomes 𝑓: 0.031 ( 902 hom. )
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.53
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 made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.111 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
use as main transcript | n.42315419T>C | intergenic_region | ||||||
TFF3 | NM_003226.4 | c.-45A>G | upstream_gene_variant | ENST00000518498.3 | NP_003217.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TFF3 | ENST00000518498.3 | c.-45A>G | upstream_gene_variant | 1 | NM_003226.4 | ENSP00000430690.2 |
Frequencies
GnomAD3 genomes AF: 0.0517 AC: 7865AN: 152160Hom.: 325 Cov.: 32
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GnomAD3 exomes AF: 0.0282 AC: 7101AN: 251482Hom.: 201 AF XY: 0.0258 AC XY: 3513AN XY: 135918
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GnomAD4 exome AF: 0.0309 AC: 45106AN: 1461856Hom.: 902 Cov.: 31 AF XY: 0.0300 AC XY: 21835AN XY: 727228
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GnomAD4 genome AF: 0.0517 AC: 7877AN: 152278Hom.: 325 Cov.: 32 AF XY: 0.0490 AC XY: 3650AN XY: 74462
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at