rs4444493
Positions:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_003597.5(KLF11):c.*544C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0939 in 392,436 control chromosomes in the GnomAD database, including 2,130 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.084 ( 680 hom., cov: 33)
Exomes 𝑓: 0.10 ( 1450 hom. )
Consequence
KLF11
NM_003597.5 3_prime_UTR
NM_003597.5 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.558
Genes affected
KLF11 (HGNC:11811): (KLF transcription factor 11) The protein encoded by this gene is a zinc finger transcription factor that binds to SP1-like sequences in epsilon- and gamma-globin gene promoters. This binding inhibits cell growth and causes apoptosis. Defects in this gene are a cause of maturity-onset diabetes of the young type 7 (MODY7). Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Apr 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
?
Variant 2-10053051-C-A is Benign according to our data. Variant chr2-10053051-C-A is described in ClinVar as [Benign]. Clinvar id is 330654.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.117 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KLF11 | NM_003597.5 | c.*544C>A | 3_prime_UTR_variant | 4/4 | ENST00000305883.6 | ||
KLF11 | NM_001177716.2 | c.*544C>A | 3_prime_UTR_variant | 4/4 | |||
KLF11 | NM_001177718.2 | c.*544C>A | 3_prime_UTR_variant | 4/4 | |||
KLF11 | XM_047446025.1 | c.*544C>A | 3_prime_UTR_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KLF11 | ENST00000305883.6 | c.*544C>A | 3_prime_UTR_variant | 4/4 | 1 | NM_003597.5 | A2 | ||
KLF11 | ENST00000535335.1 | c.*544C>A | 3_prime_UTR_variant | 4/4 | 2 | P4 | |||
KLF11 | ENST00000540845.5 | c.*544C>A | 3_prime_UTR_variant | 4/4 | 2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0838 AC: 12748AN: 152120Hom.: 680 Cov.: 33
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GnomAD4 exome AF: 0.100 AC: 24105AN: 240198Hom.: 1450 Cov.: 0 AF XY: 0.101 AC XY: 12357AN XY: 121834
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GnomAD4 genome ? AF: 0.0837 AC: 12749AN: 152238Hom.: 680 Cov.: 33 AF XY: 0.0808 AC XY: 6016AN XY: 74416
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Maturity-onset diabetes of the young type 7 Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at