Variant 2-10043427-C-CGGCCGGGCACG details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

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

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.419

Variant links:

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 links:

KLF11-DT (HGNC:):

KLF11-DT links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

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	Protein	UniProt
KLF11-DT	NR_135558.1 linkuse as main transcript			upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KLF11	ENST00000401510.5 linkuse as main transcript	c.-10+357_-10+367dup		intron_variant		3		ENSP00000386058

Frequencies

GnomAD3 genomes

AF:

0.856

AC:

124200

AN:

145092

Hom.:

53483

Cov.:

show subpopulations

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:

AN:

Hom.:

AF XY:

0.571

AC XY:

AN XY:

show subpopulations

Gnomad4 SAS exome

AF:

0.750

Gnomad4 NFE exome

AF:

0.542

GnomAD4 genome

AF:

0.856

AC:

124302

AN:

145180

Hom.:

53538

Cov.:

AF XY:

0.859

AC XY:

60639

AN XY:

70618

show subpopulations

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

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 17, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over