2-207166591-G-T

Position:

• chr2-207166591-G-T

Variant summary

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

The NM_001270943.2(KLF7):​c.3+549C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.377 in 157,254 control chromosomes in the GnomAD database, including 11,970 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 0.38 (11564 hom., cov: 28)
  • Exomes 𝑓: 0.35 (406 hom.)
• Consequence: KLF7 NM_001270943.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0740

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]

MYOSLID (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.508 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KLF7	NM_001270943.2	c.3+549C>A		intron_variant			NP_001257872.1
KLF7	NM_001270942.1	c.-139+166C>A		intron_variant			NP_001257871.1
KLF7	XM_047446144.1	c.-139+166C>A		intron_variant			XP_047302100.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KLF7	ENST00000421199.5	c.3+549C>A		intron_variant		1		ENSP00000387510.1
KLF7	ENST00000423015.5	c.-139+166C>A		intron_variant		1		ENSP00000398572.1
KLF7	ENST00000703736.1	c.3+549C>A		intron_variant				ENSP00000515456.1

Frequencies

GnomAD3 genomes AF: 0.378 AC: 56912 AN: 150386 Hom.: 11549 Cov.: 28

Gnomad AFR AF: 0.513

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.400

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.384

GnomAD4 exome AF: 0.346 AC: 2342 AN: 6760 Hom.: 406 Cov.: 4 AF XY: 0.339 AC XY: 1121 AN XY: 3308

Gnomad4 AFR exome AF: 0.555

Gnomad4 AMR exome AF: 0.167

Gnomad4 ASJ exome AF: 0.340

Gnomad4 EAS exome AF: 0.125

Gnomad4 SAS exome AF: 0.354

Gnomad4 NFE exome AF: 0.345

Gnomad4 OTH exome AF: 0.306

GnomAD4 genome AF: 0.379 AC: 56967 AN: 150494 Hom.: 11564 Cov.: 28 AF XY: 0.373 AC XY: 27376 AN XY: 73492

Gnomad4 AFR AF: 0.514

Gnomad4 AMR AF: 0.298

Gnomad4 ASJ AF: 0.336

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.318

Gnomad4 FIN AF: 0.333

Gnomad4 NFE AF: 0.346

Gnomad4 OTH AF: 0.380

Alfa AF: 0.366 Hom.: 1301

Bravo AF: 0.381

Asia WGS AF: 0.211 AC: 732 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	8.0
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7568369; hg19: chr2-208031315;