rs112040334

Variant names:

• chr2-10043427-C-CGGCCGGGCACG
• rs112040334
• ENST00000401510.5:c.-10+357_-10+367dupGGCCGGGCACG

Your query was ambiguous. Multiple possible variants found:

• chr2-10043427-C-CGGCCGGGCACG
• chr2-10043427-C-CGGCCGGGCACGGGCCGGGCACG

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The ENST00000401510.5(KLF11):​c.-10+357_-10+367dupGGCCGGGCACG variant causes a intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. 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
• Publications: 3 publications found

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]

ENSG00000260077 (HGNC:):

KLF11-DT (HGNC:56037): (KLF11 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000401510.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KLF11	NM_003597.5	MANE Select	c.-290_-289insGGCCGGGCACG		upstream_gene	N/A	NP_003588.1	O14901-1
	KLF11-DT	NR_135558.1		n.-27_-26insCGTGCCCGGCC		upstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KLF11	ENST00000401510.5	TSL:3	c.-10+357_-10+367dupGGCCGGGCACG		intron	N/A	ENSP00000386058.1	B5MCC4
	ENSG00000260077	ENST00000567540.2	TSL:6	n.5_15dupCGTGCCCGGCC		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000260077	ENST00000837798.1		n.9_19dupCGTGCCCGGCC		non_coding_transcript_exon	Exon 1 of 6

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.750 AC: 3 AN: 4

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.542 AC: 13 AN: 24

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.944 AC: 38119 AN: 40396

American (AMR) AF: 0.879 AC: 12962 AN: 14752

Ashkenazi Jewish (ASJ) AF: 0.859 AC: 2897 AN: 3374

East Asian (EAS) AF: 0.840 AC: 4118 AN: 4900

South Asian (SAS) AF: 0.823 AC: 3909 AN: 4748

European-Finnish (FIN) AF: 0.877 AC: 7410 AN: 8454

Middle Eastern (MID) AF: 0.902 AC: 258 AN: 286

European-Non Finnish (NFE) AF: 0.799 AC: 52188 AN: 65352

Other (OTH) AF: 0.856 AC: 1725 AN: 2016

Alfa AF: 0.809 Hom.: 1688

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.42
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs112040334; hg19: chr2-10183554;