2-10043621-TGCCGCCGCC-T

Variant names:

• chr2-10043621-TGCCGCCGCC-T
• rs372827624
• NM_003597.5:c.-86_-78delGCCGCCGCC

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_003597.5(KLF11):​c.-86_-78delGCCGCCGCC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000576 in 867,586 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0000069 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0000055 (0 hom.)
• Consequence: KLF11 NM_003597.5 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06

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:56037): (KLF11 divergent transcript)

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KLF11	NM_003597.5	c.-86_-78delGCCGCCGCC		5_prime_UTR_variant	Exon 1 of 4	ENST00000305883.6	NP_003588.1
KLF11	NM_001177716.2	c.-275_-267delGCCGCCGCC		upstream_gene_variant			NP_001171187.1
KLF11-DT	NR_135558.1	n.-229_-221delGGCGGCGGC		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KLF11	ENST00000305883	c.-86_-78delGCCGCCGCC		5_prime_UTR_variant	Exon 1 of 4	1	NM_003597.5	ENSP00000307023.1
KLF11	ENST00000401510.5	c.-10+560_-10+568delGCCGCCGCC		intron_variant	Intron 1 of 2	3		ENSP00000386058.1
KLF11	ENST00000540845.5	c.-275_-267delGCCGCCGCC		upstream_gene_variant		2		ENSP00000444690.1
KLF11	ENST00000448523.5	c.-275_-267delGCCGCCGCC		upstream_gene_variant		4		ENSP00000387866.1

Frequencies

GnomAD3 genomes AF: 0.00000692 AC: 1 AN: 144576 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000153

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00000553 AC: 4 AN: 723010 Hom.: 0 AF XY: 0.00000870 AC XY: 3 AN XY: 344874

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000613

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.00000692 AC: 1 AN: 144576 Hom.: 0 Cov.: 0 AF XY: 0.0000142 AC XY: 1 AN XY: 70238

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000153

Gnomad4 OTH AF: 0.00

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

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: rs372827624; hg19: chr2-10183748;