2-10043427-C-CGGCCGGGCACG

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The ENST00000401510.5(KLF11):c.-10+357_-10+367dup variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.86 (53538 hom., cov: 0)
  • Exomes 𝑓: 0.57 (5 hom.)
  • Failed GnomAD Quality Control
• Consequence: KLF11 ENST00000401510.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.419

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]

KLF11-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 2-10043427-C-CGGCCGGGCACG is Benign according to our data. Variant chr2-10043427-C-CGGCCGGGCACG is described in ClinVar as [Benign]. Clinvar id is 1264076.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.936 is higher than 0.05.

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+357_-10+367dup		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.856 AC: 124200 AN: 145092 Hom.: 53483 Cov.: 0

Gnomad AFR AF: 0.943

Gnomad AMI AF: 0.794

Gnomad AMR AF: 0.878

Gnomad ASJ AF: 0.859

Gnomad EAS AF: 0.840

Gnomad SAS AF: 0.823

Gnomad FIN AF: 0.877

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.799

Gnomad OTH AF: 0.853

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.571 AC: 16 AN: 28 Hom.: 5 AF XY: 0.571 AC XY: 8 AN XY: 14

Gnomad4 SAS exome AF: 0.750

Gnomad4 NFE exome AF: 0.542

GnomAD4 genome AF: 0.856 AC: 124302 AN: 145180 Hom.: 53538 Cov.: 0 AF XY: 0.859 AC XY: 60639 AN XY: 70618

Gnomad4 AFR AF: 0.944

Gnomad4 AMR AF: 0.879

Gnomad4 ASJ AF: 0.859

Gnomad4 EAS AF: 0.840

Gnomad4 SAS AF: 0.823

Gnomad4 FIN AF: 0.877

Gnomad4 NFE AF: 0.799

Gnomad4 OTH AF: 0.856

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 17, 2018

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Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs112040334; hg19: chr2-10183554;