rs2244399

chr2-207114326-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003709.4(KLF7):c.733+9448A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 152,214 control chromosomes in the GnomAD database, including 2,743 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.18 (2743 hom., cov: 32)
• Consequence: KLF7 NM_003709.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.105

Genes affected

KLF7 (HGNC:6350): (KLF transcription factor 7) The protein encoded by this gene is a member of the Kruppel-like transcriptional regulator family. Members in this family regulate cell proliferation, differentiation and survival and contain three C2H2 zinc fingers at the C-terminus that mediate binding to GC-rich sites. This protein may contribute to the progression of type 2 diabetes by inhibiting insulin expression and secretion in pancreatic beta-cells and by deregulating adipocytokine secretion in adipocytes. A pseudogene of this gene is located on the long arm of chromosome 3. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.315 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KLF7	NM_003709.4	c.733+9448A>G		intron_variant		ENST00000309446.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KLF7	ENST00000309446.11	c.733+9448A>G		intron_variant		1	NM_003709.4	P1

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27711 AN: 152096 Hom.: 2743 Cov.: 32

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.158

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.182 AC: 27721 AN: 152214 Hom.: 2743 Cov.: 32 AF XY: 0.183 AC XY: 13591 AN XY: 74434

Gnomad4 AFR AF: 0.217

Gnomad4 AMR AF: 0.101

Gnomad4 ASJ AF: 0.159

Gnomad4 EAS AF: 0.328

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.160

Alfa AF: 0.166 Hom.: 3681

Bravo AF: 0.177

Asia WGS AF: 0.309 AC: 1071 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
Cadd	Benign	8.4
Dann	Benign	0.74

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2244399; hg19: chr2-207979050;