9-5059440-C-T

Variant names:

• chr9-5059440-C-T
• rs2149556
• NM_004972.4:c.1056+3652C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004972.4(JAK2):​c.1056+3652C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.63 in 152,004 control chromosomes in the GnomAD database, including 32,186 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 0.63 (32186 hom., cov: 32)
• Consequence: JAK2 NM_004972.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.529
• Publications: 10 publications found

Genes affected

JAK2 (HGNC:6192): (Janus kinase 2) This gene encodes a non-receptor tyrosine kinase that plays a central role in cytokine and growth factor signalling. The primary isoform of this protein has an N-terminal FERM domain that is required for erythropoietin receptor association, an SH2 domain that binds STAT transcription factors, a pseudokinase domain and a C-terminal tyrosine kinase domain. Cytokine binding induces autophosphorylation and activation of this kinase. This kinase then recruits and phosphorylates signal transducer and activator of transcription (STAT) proteins. Growth factors like TGF-beta 1 also induce phosphorylation and activation of this kinase and translocation of downstream STAT proteins to the nucleus where they influence gene transcription. Mutations in this gene are associated with numerous inflammatory diseases and malignancies. This gene is a downstream target of the pleiotropic cytokine IL6 that is produced by B cells, T cells, dendritic cells and macrophages to produce an immune response or inflammation. Disregulation of the IL6/JAK2/STAT3 signalling pathways produces increased cellular proliferation and myeloproliferative neoplasms of hematopoietic stem cells. A nonsynonymous mutation in the pseudokinase domain of this gene disrupts the domains inhibitory effect and results in constitutive tyrosine phosphorylation activity and hypersensitivity to cytokine signalling. This gene and the IL6/JAK2/STAT3 signalling pathway is a therapeutic target for the treatment of excessive inflammatory responses to viral infections. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2020]

INSL6 (HGNC:6089): (insulin like 6) The protein encoded by this gene contains a classical signature of the insulin superfamily and is significantly similar to relaxin and relaxin-like factor. This gene is preferentially expressed in testis. Its expression in testis is restricted to interstitial cells surrounding seminiferous tubules, which suggests a role in sperm development and fertilization. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.873 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004972.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	JAK2	NM_004972.4	MANE Select	c.1056+3652C>T		intron	N/A	NP_004963.1
	JAK2	NM_001322194.2		c.1056+3652C>T		intron	N/A	NP_001309123.1
	JAK2	NM_001322195.2		c.1056+3652C>T		intron	N/A	NP_001309124.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	JAK2	ENST00000381652.4	TSL:1 MANE Select	c.1056+3652C>T		intron	N/A	ENSP00000371067.4
	JAK2	ENST00000870320.1		c.1056+3652C>T		intron	N/A	ENSP00000540379.1
	JAK2	ENST00000870321.1		c.1056+3652C>T		intron	N/A	ENSP00000540380.1

Frequencies

GnomAD3 genomes AF: 0.630 AC: 95622 AN: 151886 Hom.: 32137 Cov.: 32

Gnomad AFR AF: 0.881

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.579

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.509

Gnomad OTH AF: 0.608

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.630 AC: 95727 AN: 152004 Hom.: 32186 Cov.: 32 AF XY: 0.631 AC XY: 46869 AN XY: 74268

African (AFR) AF: 0.881 AC: 36572 AN: 41516

American (AMR) AF: 0.565 AC: 8618 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.586 AC: 2030 AN: 3464

East Asian (EAS) AF: 0.524 AC: 2707 AN: 5170

South Asian (SAS) AF: 0.579 AC: 2786 AN: 4812

European-Finnish (FIN) AF: 0.614 AC: 6480 AN: 10546

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.509 AC: 34560 AN: 67930

Other (OTH) AF: 0.610 AC: 1286 AN: 2108

Alfa AF: 0.584 Hom.: 4525

Bravo AF: 0.634

Asia WGS AF: 0.621 AC: 2152 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.76
DANN	Benign	0.20
PhyloP100		-0.53
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2149556; hg19: chr9-5059440;