dbSNP rs566045982: IDNK:p.Pro4Arg (chr9-83623182-C-G) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001001551.4(IDNK):c.11C>G(p.Pro4Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000113 in 1,413,504 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000046 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0000071 ( 0 hom. )

Consequence

IDNK
NM_001001551.4 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.277

Publications

1 publications found

Variant links:

Genes affected

IDNK (HGNC:31367): (IDNK gluconokinase) Predicted to enable gluconokinase activity. Predicted to be involved in D-gluconate catabolic process. [provided by Alliance of Genome Resources, Apr 2022]

IDNK links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.026270956).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001001551.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
IDNK	NM_001001551.4	MANE Select	c.11C>G	p.Pro4Arg	missense	Exon 1 of 5	NP_001001551.2	Q5T6J7-1
IDNK	NM_001256915.2		c.-302C>G		5_prime_UTR	Exon 1 of 5	NP_001243844.1	Q5T6J7-3
IDNK	NM_001351535.2		c.-200C>G		5_prime_UTR	Exon 1 of 5	NP_001338464.1	Q5T6J7-3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
IDNK	ENST00000376419.5	TSL:1 MANE Select	c.11C>G	p.Pro4Arg	missense	Exon 1 of 5	ENSP00000365601.4	Q5T6J7-1
IDNK	ENST00000533522.1	TSL:1	n.11C>G		non_coding_transcript_exon	Exon 1 of 6	ENSP00000434673.1	E9PP88
IDNK	ENST00000904784.1		c.11C>G	p.Pro4Arg	missense	Exon 1 of 5	ENSP00000574843.1

Frequencies

GnomAD3 genomes

AF:

0.0000461

AC:

AN:

151908

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00136

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.0000416

AC:

AN:

24044

AF XY:

0.00

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00262

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000713

AC:

AN:

1261482

Hom.:

Cov.:

AF XY:

0.00000649

AC XY:

AN XY:

616406

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

24270

American (AMR)

AF:

0.00

AC:

AN:

12296

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

18308

East Asian (EAS)

AF:

0.000180

AC:

AN:

27716

South Asian (SAS)

AF:

0.00

AC:

AN:

57406

European-Finnish (FIN)

AF:

0.00

AC:

AN:

43732

Middle Eastern (MID)

AF:

0.000219

AC:

AN:

4576

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1021486

Other (OTH)

AF:

0.0000580

AC:

AN:

51692

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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:

0.0000460

AC:

AN:

152022

Hom.:

Cov.:

AF XY:

0.0000538

AC XY:

AN XY:

74306

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

41502

American (AMR)

AF:

0.00

AC:

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3472

East Asian (EAS)

AF:

0.00136

AC:

AN:

5132

South Asian (SAS)

AF:

0.00

AC:

AN:

4826

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10580

Middle Eastern (MID)

AF:

0.00

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

67906

Other (OTH)

AF:

0.00

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

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

Alfa

AF:

0.00

Hom.:

Bravo

AF:

0.000110

ClinVar

ClinVar submissions

Significance:Uncertain significance

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.16

BayesDel_addAF

Benign

-0.47

BayesDel_noAF

Benign

-0.45

CADD

Benign

(source)

DANN

Uncertain

0.99

DEOGEN2

Benign

0.033

Eigen

Benign

-0.41

Eigen_PC

Benign

-0.61

FATHMM_MKL

Benign

0.10

LIST_S2

Benign

0.41

M_CAP

Benign

0.039

MetaRNN

Benign

0.026

MetaSVM

Benign

-0.98

MutationAssessor

Benign

1.5

PhyloP100

0.28

PrimateAI

Pathogenic

0.81

PROVEAN

Pathogenic

-9.0

REVEL

Benign

0.065

Sift

Uncertain

0.0020

Sift4G

Benign

0.071

Polyphen

1.0

Vest4

0.23

MutPred

0.41

Gain of MoRF binding (P = 2e-04)

MVP

0.20

MPC

0.56

ClinPred

0.48

GERP RS

2.6

PromoterAI

-0.34

Neutral

(source)

Varity_R

0.12

gMVP

0.64

Mutation Taster

=94/6

polymorphism

(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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over