rs1046917

Positions:

• chr17-82727779-A-G

Variant summary

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

The NM_024619.4(FN3KRP):​c.*608A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.685 in 152,124 control chromosomes in the GnomAD database, including 35,965 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 0.69 (35937 hom., cov: 33)
  • Exomes 𝑓: 0.61 (28 hom.)
• Consequence: FN3KRP NM_024619.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47

Genes affected

FN3KRP (HGNC:25700): (fructosamine 3 kinase related protein) A high concentration of glucose can result in non-enzymatic oxidation of proteins by reaction of glucose and lysine residues (glycation). Proteins modified in this way are less active or functional. This gene encodes an enzyme which catalyzes the phosphorylation of psicosamines and ribulosamines compared to the neighboring gene which encodes a highly similar enzyme, fructosamine-3-kinase, which has different substrate specificity. The activity of both enzymes may result in deglycation of proteins to restore their function. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.735 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FN3KRP	NM_024619.4	c.*608A>G		3_prime_UTR_variant	6/6	ENST00000269373.11	NP_078895.2
FN3KRP	NR_046408.2	n.1716A>G		non_coding_transcript_exon_variant	7/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FN3KRP	ENST00000269373.11	c.*608A>G		3_prime_UTR_variant	6/6	1	NM_024619.4	ENSP00000269373	P1
FN3KRP	ENST00000571594.1	c.53+612A>G		intron_variant, NMD_transcript_variant		3		ENSP00000459751

Frequencies

GnomAD3 genomes AF: 0.685 AC: 104088 AN: 151866 Hom.: 35919 Cov.: 33

Gnomad AFR AF: 0.742

Gnomad AMI AF: 0.728

Gnomad AMR AF: 0.610

Gnomad ASJ AF: 0.635

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.735

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.644

GnomAD4 exome AF: 0.607 AC: 85 AN: 140 Hom.: 28 Cov.: 0 AF XY: 0.544 AC XY: 37 AN XY: 68

Gnomad4 AFR exome AF: 0.500

Gnomad4 AMR exome AF: 0.167

Gnomad4 SAS exome AF: 0.250

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.652

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.685 AC: 104153 AN: 151984 Hom.: 35937 Cov.: 33 AF XY: 0.684 AC XY: 50790 AN XY: 74302

Gnomad4 AFR AF: 0.742

Gnomad4 AMR AF: 0.609

Gnomad4 ASJ AF: 0.635

Gnomad4 EAS AF: 0.502

Gnomad4 SAS AF: 0.614

Gnomad4 FIN AF: 0.735

Gnomad4 NFE AF: 0.683

Gnomad4 OTH AF: 0.638

Alfa AF: 0.661 Hom.: 28943

Bravo AF: 0.677

Asia WGS AF: 0.565 AC: 1968 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.37
DANN	Benign	0.28
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs1046917; hg19: chr17-80685655; COSMIC: COSV105033952; COSMIC: COSV105033952;