chr2-207124261-G-A
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Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_003709.4(KLF7):c.246C>T(p.Leu82=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00486 in 1,614,136 control chromosomes in the GnomAD database, including 28 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0038 ( 2 hom., cov: 31)
Exomes 𝑓: 0.0050 ( 26 hom. )
Consequence
KLF7
NM_003709.4 synonymous
NM_003709.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.306
Genes affected
KLF7 (HGNC:6350): (KLF transcription factor 7) The protein encoded by this gene is a member of the Kruppel-like transcriptional regulator family. Members in this family regulate cell proliferation, differentiation and survival and contain three C2H2 zinc fingers at the C-terminus that mediate binding to GC-rich sites. This protein may contribute to the progression of type 2 diabetes by inhibiting insulin expression and secretion in pancreatic beta-cells and by deregulating adipocytokine secretion in adipocytes. A pseudogene of this gene is located on the long arm of chromosome 3. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.5).
BP6
Variant 2-207124261-G-A is Benign according to our data. Variant chr2-207124261-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 789158.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=0.306 with no splicing effect.
BS2
High AC in GnomAd4 at 583 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KLF7 | NM_003709.4 | c.246C>T | p.Leu82= | synonymous_variant | 2/4 | ENST00000309446.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KLF7 | ENST00000309446.11 | c.246C>T | p.Leu82= | synonymous_variant | 2/4 | 1 | NM_003709.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00383 AC: 582AN: 152134Hom.: 2 Cov.: 31
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GnomAD3 exomes AF: 0.00377 AC: 946AN: 251144Hom.: 5 AF XY: 0.00394 AC XY: 535AN XY: 135818
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GnomAD4 exome AF: 0.00496 AC: 7258AN: 1461884Hom.: 26 Cov.: 36 AF XY: 0.00483 AC XY: 3509AN XY: 727238
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GnomAD4 genome AF: 0.00383 AC: 583AN: 152252Hom.: 2 Cov.: 31 AF XY: 0.00416 AC XY: 310AN XY: 74440
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
KLF7-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 14, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Mar 05, 2018 | - - |
Computational scores
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BayesDel_noAF
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CADD
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DANN
Benign
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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