rs11086029

chr19-16327850-T-Achr19-16327850-T-G

Variant summary

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

The NM_016270.4(KLF2):c.*819T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.778 in 151,316 control chromosomes in the GnomAD database, including 46,036 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 0.78 (46033 hom., cov: 30)
  • Exomes 𝑓: 0.80 (3 hom.)
• Consequence: KLF2 NM_016270.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.509

Genes affected

KLF2 (HGNC:6347): (KLF transcription factor 2) This gene encodes a protein that belongs to the Kruppel family of transcription factors. The encoded zinc finger protein is expressed early in mammalian development and is found in many different cell types. The protein acts to bind the CACCC box found in the promoter of target genes to activate their transcription. It plays a role in many processes during development and disease including adipogenesis, embryonic erythropoiesis, epithelial integrity, inflammation and t-cell viability. [provided by RefSeq, Mar 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.808 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KLF2	NM_016270.4	c.*819T>A		3_prime_UTR_variant	3/3	ENST00000248071.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KLF2	ENST00000248071.6	c.*819T>A		3_prime_UTR_variant	3/3	1	NM_016270.4	P1

Frequencies

GnomAD3 genomes AF: 0.778 AC: 117601 AN: 151196 Hom.: 46009 Cov.: 30

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.801

Gnomad AMR AF: 0.813

Gnomad ASJ AF: 0.837

Gnomad EAS AF: 0.577

Gnomad SAS AF: 0.722

Gnomad FIN AF: 0.794

Gnomad MID AF: 0.825

Gnomad NFE AF: 0.760

Gnomad OTH AF: 0.785

GnomAD4 exome AF: 0.800 AC: 8 AN: 10 Hom.: 3 Cov.: 0 AF XY: 0.667 AC XY: 4 AN XY: 6

Gnomad4 SAS exome AF: 0.667

Gnomad4 NFE exome AF: 1.00

GnomAD4 genome AF: 0.778 AC: 117676 AN: 151306 Hom.: 46033 Cov.: 30 AF XY: 0.777 AC XY: 57422 AN XY: 73918

Gnomad4 AFR AF: 0.815

Gnomad4 AMR AF: 0.813

Gnomad4 ASJ AF: 0.837

Gnomad4 EAS AF: 0.578

Gnomad4 SAS AF: 0.723

Gnomad4 FIN AF: 0.794

Gnomad4 NFE AF: 0.760

Gnomad4 OTH AF: 0.778

Alfa AF: 0.694 Hom.: 1548

Bravo AF: 0.784

Asia WGS AF: 0.663 AC: 2306 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.5
Dann	Benign	0.54

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: rs11086029; hg19: chr19-16438661;