rs8810

chr19-16327504-A-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_016270.4(KLF2):c.*473A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 151,138 control chromosomes in the GnomAD database, including 5,128 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 0.24 (5106 hom., cov: 31)
  • Exomes 𝑓: 0.20 (22 hom.)
• Consequence: KLF2 NM_016270.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.21

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.31).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KLF2	NM_016270.4	c.*473A>T		3_prime_UTR_variant	3/3	ENST00000248071.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KLF2	ENST00000248071.6	c.*473A>T		3_prime_UTR_variant	3/3	1	NM_016270.4	P1

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36462 AN: 150336 Hom.: 5108 Cov.: 31

Gnomad AFR AF: 0.0922

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.328

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.264

GnomAD4 exome AF: 0.204 AC: 141 AN: 690 Hom.: 22 Cov.: 0 AF XY: 0.237 AC XY: 103 AN XY: 434

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.147

Gnomad4 ASJ exome AF: 0.300

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.284

Gnomad4 FIN exome AF: 0.214

Gnomad4 NFE exome AF: 0.174

Gnomad4 OTH exome AF: 0.154

GnomAD4 genome AF: 0.242 AC: 36462 AN: 150448 Hom.: 5106 Cov.: 31 AF XY: 0.244 AC XY: 17926 AN XY: 73464

Gnomad4 AFR AF: 0.0919

Gnomad4 AMR AF: 0.317

Gnomad4 ASJ AF: 0.286

Gnomad4 EAS AF: 0.255

Gnomad4 SAS AF: 0.391

Gnomad4 FIN AF: 0.243

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.263

Alfa AF: 0.259 Hom.: 538

Bravo AF: 0.238

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
Cadd	Benign	16
Dann	Benign	0.90

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: rs8810; hg19: chr19-16438315;