Genetic Variant FN3K:p.Ser300Ser (chr17-82750725-C-G) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_022158.4(FN3K):c.900C>G(p.Ser300Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.612 in 1,612,850 control chromosomes in the GnomAD database, including 302,159 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 0.62 ( 29574 hom., cov: 29)

Exomes 𝑓: 0.61 ( 272585 hom. )

Consequence

FN3K
NM_022158.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.882

Publications

39 publications found

Variant links:

Genes affected

FN3K (HGNC:24822): (fructosamine 3 kinase) 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, fructosamines, are less active or functional. This gene encodes an enzyme which catalyzes the phosphorylation of fructosamines which may result in deglycation. [provided by RefSeq, Feb 2012]

FN3K links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BP7

Synonymous conserved (PhyloP=-0.882 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FN3K	NM_022158.4 link	c.900C>G	p.Ser300Ser	synonymous_variant	Exon 6 of 6	ENST00000300784.8	NP_071441.1	Q9H479

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FN3K	ENST00000300784.8 link	c.900C>G	p.Ser300Ser	synonymous_variant	Exon 6 of 6	1	NM_022158.4	ENSP00000300784.7		Q9H479

Frequencies

GnomAD3 genomes

AF:

0.623

AC:

94487

AN:

151580

Hom.:

29518

Cov.:

show subpopulations

Gnomad AFR

AF:

0.654

Gnomad AMI

AF:

0.646

Gnomad AMR

AF:

0.592

Gnomad ASJ

AF:

0.626

Gnomad EAS

AF:

0.622

Gnomad SAS

AF:

0.642

Gnomad FIN

AF:

0.608

Gnomad MID

AF:

0.595

Gnomad NFE

AF:

0.613

Gnomad OTH

AF:

0.622

GnomAD2 exomes

AF:

0.618

AC:

154749

AN:

250364

AF XY:

0.620

show subpopulations

Gnomad AFR exome

AF:

0.657

Gnomad AMR exome

AF:

0.581

Gnomad ASJ exome

AF:

0.623

Gnomad EAS exome

AF:

0.631

Gnomad FIN exome

AF:

0.611

Gnomad NFE exome

AF:

0.614

Gnomad OTH exome

AF:

0.614

GnomAD4 exome

AF:

0.610

AC:

891727

AN:

1461150

Hom.:

272585

Cov.:

AF XY:

0.612

AC XY:

444872

AN XY:

726902

show subpopulations

African (AFR)

AF:

0.658

AC:

22029

AN:

33478

American (AMR)

AF:

0.581

AC:

25977

AN:

44720

Ashkenazi Jewish (ASJ)

AF:

0.631

AC:

16491

AN:

26122

East Asian (EAS)

AF:

0.616

AC:

24453

AN:

39700

South Asian (SAS)

AF:

0.647

AC:

55829

AN:

86254

European-Finnish (FIN)

AF:

0.610

AC:

32243

AN:

52862

Middle Eastern (MID)

AF:

0.612

AC:

3524

AN:

5762

European-Non Finnish (NFE)

AF:

0.606

AC:

674006

AN:

1111868

Other (OTH)

AF:

0.616

AC:

37175

AN:

60384

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.487

Heterozygous variant carriers

19564

39128

58693

78257

97821

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.624

AC:

94604

AN:

151700

Hom.:

29574

Cov.:

AF XY:

0.624

AC XY:

46281

AN XY:

74128

show subpopulations

African (AFR)

AF:

0.654

AC:

27058

AN:

41342

American (AMR)

AF:

0.592

AC:

9040

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.626

AC:

2171

AN:

3466

East Asian (EAS)

AF:

0.621

AC:

3170

AN:

5104

South Asian (SAS)

AF:

0.643

AC:

3084

AN:

4794

European-Finnish (FIN)

AF:

0.608

AC:

6419

AN:

10564

Middle Eastern (MID)

AF:

0.585

AC:

172

AN:

294

European-Non Finnish (NFE)

AF:

0.613

AC:

41583

AN:

67854

Other (OTH)

AF:

0.626

AC:

1319

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1764

3528

5292

7056

8820

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.622

Hom.:

9539

Bravo

AF:

0.621

Asia WGS

AF:

0.648

AC:

2252

AN:

3478

EpiCase

AF:

0.612

EpiControl

AF:

0.605

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

1.1

(source)

DANN

Benign

0.66

PhyloP100

-0.88

RBP_binding_hub_radar

0.97

RBP_regulation_power_radar

4.0

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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17-82750725-C-G

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