1-64883298-T-C

Variant names:

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_002227.4(JAK1):c.184A>G(p.Ile62Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000483 in 1,614,016 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 17/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.00043 ( 0 hom., cov: 32)

Exomes 𝑓: 0.00049 ( 2 hom. )

Consequence

JAK1
NM_002227.4 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1O:1

Conservation

PhyloP100: 1.89

Publications

12 publications found

Variant links:

Genes affected

JAK1 (HGNC:6190): (Janus kinase 1) This gene encodes a membrane protein that is a member of a class of protein-tyrosine kinases (PTK) characterized by the presence of a second phosphotransferase-related domain immediately N-terminal to the PTK domain. The encoded kinase phosphorylates STAT proteins (signal transducers and activators of transcription) and plays a key role in interferon-alpha/beta, interferon-gamma, and cytokine signal transduction. This gene plays a crucial role in effecting the expression of genes that mediate inflammation, epithelial remodeling, and metastatic cancer progression. This gene is a key component of the interleukin-6 (IL-6)/JAK1/STAT3 immune and inflammation response and is a therapeutic target for alleviating cytokine storms. The kinase activity of this gene is directly inhibited by the suppressor of cytokine signalling 1 (SOCS1) protein. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2020]

JAK1 Gene-Disease associations (from GenCC):

autoinflammation, immune dysregulation, and eosinophilia
Inheritance: AD Classification: STRONG, MODERATE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)

JAK1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.008037269).

BP6

Variant 1-64883298-T-C is Benign according to our data. Variant chr1-64883298-T-C is described in CliVar as Benign. Clinvar id is 134548.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-64883298-T-C is described in CliVar as Benign. Clinvar id is 134548.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-64883298-T-C is described in CliVar as Benign. Clinvar id is 134548.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-64883298-T-C is described in CliVar as Benign. Clinvar id is 134548.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-64883298-T-C is described in CliVar as Benign. Clinvar id is 134548.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-64883298-T-C is described in CliVar as Benign. Clinvar id is 134548.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-64883298-T-C is described in CliVar as Benign. Clinvar id is 134548.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-64883298-T-C is described in CliVar as Benign. Clinvar id is 134548.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-64883298-T-C is described in CliVar as Benign. Clinvar id is 134548.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-64883298-T-C is described in CliVar as Benign. Clinvar id is 134548.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-64883298-T-C is described in CliVar as Benign. Clinvar id is 134548.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-64883298-T-C is described in CliVar as Benign. Clinvar id is 134548.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-64883298-T-C is described in CliVar as Benign. Clinvar id is 134548.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-64883298-T-C is described in CliVar as Benign. Clinvar id is 134548.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-64883298-T-C is described in CliVar as Benign. Clinvar id is 134548.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-64883298-T-C is described in CliVar as Benign. Clinvar id is 134548.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-64883298-T-C is described in CliVar as Benign. Clinvar id is 134548.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-64883298-T-C is described in CliVar as Benign. Clinvar id is 134548.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-64883298-T-C is described in CliVar as Benign. Clinvar id is 134548.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-64883298-T-C is described in CliVar as Benign. Clinvar id is 134548.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-64883298-T-C is described in CliVar as Benign. Clinvar id is 134548.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-64883298-T-C is described in CliVar as Benign. Clinvar id is 134548.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-64883298-T-C is described in CliVar as Benign. Clinvar id is 134548.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-64883298-T-C is described in CliVar as Benign. Clinvar id is 134548.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-64883298-T-C is described in CliVar as Benign. Clinvar id is 134548.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-64883298-T-C is described in CliVar as Benign. Clinvar id is 134548.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-64883298-T-C is described in CliVar as Benign. Clinvar id is 134548.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-64883298-T-C is described in CliVar as Benign. Clinvar id is 134548.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-64883298-T-C is described in CliVar as Benign. Clinvar id is 134548.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-64883298-T-C is described in CliVar as Benign. Clinvar id is 134548.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-64883298-T-C is described in CliVar as Benign. Clinvar id is 134548.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-64883298-T-C is described in CliVar as Benign. Clinvar id is 134548.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-64883298-T-C is described in CliVar as Benign. Clinvar id is 134548.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-64883298-T-C is described in CliVar as Benign. Clinvar id is 134548.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-64883298-T-C is described in CliVar as Benign. Clinvar id is 134548.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-64883298-T-C is described in CliVar as Benign. Clinvar id is 134548.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-64883298-T-C is described in CliVar as Benign. Clinvar id is 134548.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-64883298-T-C is described in CliVar as Benign. Clinvar id is 134548.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-64883298-T-C is described in CliVar as Benign. Clinvar id is 134548.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-64883298-T-C is described in CliVar as Benign. Clinvar id is 134548.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-64883298-T-C is described in CliVar as Benign. Clinvar id is 134548.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High AC in GnomAd4 at 65 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
JAK1	NM_002227.4 link	c.184A>G	p.Ile62Val	missense_variant	Exon 3 of 25	ENST00000342505.5	NP_002218.2	P23458

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
JAK1	ENST00000342505.5 link	c.184A>G	p.Ile62Val	missense_variant	Exon 3 of 25	5	NM_002227.4	ENSP00000343204.4		P23458

Frequencies

GnomAD3 genomes

AF:

0.000427

AC:

AN:

152206

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000483

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000262

Gnomad ASJ

AF:

0.00720

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000456

Gnomad OTH

AF:

0.000955

GnomAD2 exomes

AF:

0.000725

AC:

180

AN:

248442

AF XY:

0.000675

show subpopulations

Gnomad AFR exome

AF:

0.0000646

Gnomad AMR exome

AF:

0.000696

Gnomad ASJ exome

AF:

0.00976

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000445

Gnomad OTH exome

AF:

0.000993

GnomAD4 exome

AF:

0.000489

AC:

715

AN:

1461692

Hom.:

Cov.:

AF XY:

0.000481

AC XY:

350

AN XY:

727124

show subpopulations

African (AFR)

AF:

0.0000597

AC:

AN:

33480

American (AMR)

AF:

0.000783

AC:

AN:

44720

Ashkenazi Jewish (ASJ)

AF:

0.0115

AC:

300

AN:

26132

East Asian (EAS)

AF:

0.00

AC:

AN:

39682

South Asian (SAS)

AF:

0.0000812

AC:

AN:

86248

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53402

Middle Eastern (MID)

AF:

0.00191

AC:

AN:

5764

European-Non Finnish (NFE)

AF:

0.000264

AC:

294

AN:

1111882

Other (OTH)

AF:

0.00109

AC:

AN:

60382

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

111

148

185

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<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:

0.000427

AC:

AN:

152324

Hom.:

Cov.:

AF XY:

0.000430

AC XY:

AN XY:

74496

show subpopulations

African (AFR)

AF:

0.0000481

AC:

AN:

41568

American (AMR)

AF:

0.000261

AC:

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.00720

AC:

AN:

3470

East Asian (EAS)

AF:

0.00

AC:

AN:

5190

South Asian (SAS)

AF:

0.000207

AC:

AN:

4832

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10622

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000456

AC:

AN:

68016

Other (OTH)

AF:

0.000945

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

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:

0.000962

Hom.:

Bravo

AF:

0.000536

TwinsUK

AF:

0.000270

AC:

ALSPAC

AF:

0.000259

AC:

ESP6500AA

AF:

0.000255

AC:

ESP6500EA

AF:

0.000604

AC:

ExAC

AF:

0.000612

AC:

EpiCase

AF:

0.000873

EpiControl

AF:

0.000653

ClinVar

Significance: Benign

Submissions summary: Benign:1Other:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Jan 28, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not specified

Other:1

Sep 19, 2013

ITMI

Significance:not provided

Review Status:no classification provided

Collection Method:reference population

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.10

BayesDel_addAF

Benign

-0.39

BayesDel_noAF

Benign

-0.43

CADD

Benign

(source)

DANN

Benign

0.94

DEOGEN2

Benign

0.28

Eigen

Benign

-0.51

Eigen_PC

Benign

-0.32

FATHMM_MKL

Uncertain

0.82

LIST_S2

Benign

0.81

M_CAP

Benign

0.0089

MetaRNN

Benign

0.0080

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.2

PhyloP100

1.9

PrimateAI

Benign

0.47

PROVEAN

Benign

0.010

REVEL

Benign

0.030

Sift

Benign

0.41

Sift4G

Benign

0.49

Polyphen

0.010

Vest4

0.21

MVP

0.49

MPC

0.49

ClinPred

0.0074

GERP RS

3.5

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.8

Varity_R

0.053

gMVP

0.21

Mutation Taster

=92/8

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over