dbSNP rs1046917: FN3KRP:c.*608A>G (chr17-82727779-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.47

Publications

15 publications found

Variant links:

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]

FN3KRP links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
FN3KRP	NM_024619.4 link	c.*608A>G		3_prime_UTR_variant	Exon 6 of 6	ENST00000269373.11	NP_078895.2
FN3KRP	NR_046408.2 link	n.1716A>G		non_coding_transcript_exon_variant	Exon 7 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FN3KRP	ENST00000269373.11 link	c.*608A>G		3_prime_UTR_variant	Exon 6 of 6	1	NM_024619.4	ENSP00000269373.6
FN3KRP	ENST00000571594.1 link	n.53+612A>G		intron_variant	Intron 1 of 2	3		ENSP00000459751.1

Frequencies

GnomAD3 genomes

AF:

0.685

AC:

104088

AN:

151866

Hom.:

35919

Cov.:

show subpopulations

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:

AN:

140

Hom.:

Cov.:

AF XY:

0.544

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AF:

0.167

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.250

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.652

AC:

AN:

112

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.515

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.685

AC:

104153

AN:

151984

Hom.:

35937

Cov.:

AF XY:

0.684

AC XY:

50790

AN XY:

74302

show subpopulations

African (AFR)

AF:

0.742

AC:

30765

AN:

41478

American (AMR)

AF:

0.609

AC:

9304

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.635

AC:

2200

AN:

3466

East Asian (EAS)

AF:

0.502

AC:

2582

AN:

5148

South Asian (SAS)

AF:

0.614

AC:

2960

AN:

4824

European-Finnish (FIN)

AF:

0.735

AC:

7758

AN:

10550

Middle Eastern (MID)

AF:

0.636

AC:

187

AN:

294

European-Non Finnish (NFE)

AF:

0.683

AC:

46387

AN:

67932

Other (OTH)

AF:

0.638

AC:

1349

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1697

3395

5092

6790

8487

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

814

1628

2442

3256

4070

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.665

Hom.:

39640

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

(source)

DANN

Benign

0.28

PhyloP100

-1.5

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over