Genetic Variant NM_003597.5:c.-86_-78dupGCCGCCGCC (chr2-10043621-T-TGCCGCCGCC) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_003597.5(KLF11):c.-86_-78dupGCCGCCGCC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000014 ( 0 hom., cov: 0)

Exomes 𝑓: 0.000017 ( 0 hom. )

Consequence

KLF11
NM_003597.5 5_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.06

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:56037): (KLF11 divergent transcript)

KLF11-DT links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BS2

High AC in GnomAdExome4 at 12 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
KLF11	NM_003597.5 link	c.-86_-78dupGCCGCCGCC	5_prime_UTR_variant	Exon 1 of 4	ENST00000305883.6	NP_003588.1	O14901-1Q53QU8
KLF11	NM_001177716.2 link	c.-276_-275insGCCGCCGCC	upstream_gene_variant			NP_001171187.1	O14901-2B7ZAX4
KLF11-DT	NR_135558.1 link	n.-229_-221dupGGCGGCGGC	upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
KLF11	ENST00000305883 link	c.-86_-78dupGCCGCCGCC	5_prime_UTR_variant	Exon 1 of 4	1	NM_003597.5	ENSP00000307023.1	O14901-1
KLF11	ENST00000401510.5 link	c.-10+560_-10+568dupGCCGCCGCC	intron_variant	Intron 1 of 2	3		ENSP00000386058.1	B5MCC4
KLF11	ENST00000540845.5 link	c.-276_-275insGCCGCCGCC	upstream_gene_variant		2		ENSP00000444690.1	O14901-2
KLF11	ENST00000448523.5 link	c.-276_-275insGCCGCCGCC	upstream_gene_variant		4		ENSP00000387866.1	E7EX78

Frequencies

GnomAD3 genomes

AF:

0.0000138

AC:

AN:

144576

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000248

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:

0.0000166

AC:

AN:

723010

Hom.:

Cov.:

AF XY:

0.00000580

AC XY:

AN XY:

344874

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.000220

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000153

Gnomad4 OTH exome

AF:

0.0000413

GnomAD4 genome

AF:

0.0000138

AC:

AN:

144576

Hom.:

Cov.:

AF XY:

0.0000142

AC XY:

AN XY:

70238

show subpopulations

Gnomad4 AFR

AF:

0.0000248

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

ClinVar

Not reported in ClinVar

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over