2-10043421-A-G
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBS1BS2
The ENST00000401510.5(KLF11):c.-10+350A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0198 in 90,554 control chromosomes in the GnomAD database, including 26 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.020 ( 25 hom., cov: 26)
Exomes 𝑓: 0.063 ( 1 hom. )
Consequence
KLF11
ENST00000401510.5 intron
ENST00000401510.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.16
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.22).
BP6
?
Variant 2-10043421-A-G is Benign according to our data. Variant chr2-10043421-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 1316851.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0197 (1786/90506) while in subpopulation NFE AF= 0.0253 (1131/44684). AF 95% confidence interval is 0.0241. There are 25 homozygotes in gnomad4. There are 821 alleles in male gnomad4 subpopulation. Median coverage is 26. This position pass quality control queck.
BS2
?
High AC in GnomAd at 1791 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KLF11-DT | NR_135558.1 | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KLF11 | ENST00000401510.5 | c.-10+350A>G | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0198 AC: 1791AN: 90456Hom.: 25 Cov.: 26
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GnomAD4 exome AF: 0.0625 AC: 3AN: 48Hom.: 1 AF XY: 0.0769 AC XY: 2AN XY: 26
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GnomAD4 genome ? AF: 0.0197 AC: 1786AN: 90506Hom.: 25 Cov.: 26 AF XY: 0.0188 AC XY: 821AN XY: 43750
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 25, 2018 | - - |
Computational scores
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Name
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Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at