chr9-5021738-G-A

Variant names:

• chr9-5021738-G-A
• rs10974919
• NM_004972.4:c.-25-225G>A

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_004972.4(JAK2):​c.-25-225G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 152,016 control chromosomes in the GnomAD database, including 6,171 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.28 (6171 hom., cov: 32)
• Consequence: JAK2 NM_004972.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.540
• Publications: 2 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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BP6: Variant 9-5021738-G-A is Benign according to our data. Variant chr9-5021738-G-A is described in ClinVar as Benign. ClinVar VariationId is 1248374.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.316 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.-25-225G>A		intron	N/A	NP_004963.1	O60674
	JAK2	NM_001322194.2		c.-25-225G>A		intron	N/A	NP_001309123.1	O60674
	JAK2	NM_001322195.2		c.-25-225G>A		intron	N/A	NP_001309124.1	O60674

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	JAK2	ENST00000381652.4	TSL:1 MANE Select	c.-25-225G>A		intron	N/A	ENSP00000371067.4	O60674
	JAK2	ENST00000870320.1		c.-25-225G>A		intron	N/A	ENSP00000540379.1
	JAK2	ENST00000870321.1		c.-25-225G>A		intron	N/A	ENSP00000540380.1

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42534 AN: 151896 Hom.: 6167 Cov.: 32

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.325

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.280 AC: 42566 AN: 152016 Hom.: 6171 Cov.: 32 AF XY: 0.275 AC XY: 20439 AN XY: 74298

African (AFR) AF: 0.320 AC: 13268 AN: 41428

American (AMR) AF: 0.260 AC: 3969 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1458 AN: 3468

East Asian (EAS) AF: 0.189 AC: 978 AN: 5174

South Asian (SAS) AF: 0.195 AC: 938 AN: 4806

European-Finnish (FIN) AF: 0.228 AC: 2418 AN: 10584

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.273 AC: 18550 AN: 67958

Other (OTH) AF: 0.287 AC: 606 AN: 2112

Alfa AF: 0.148 Hom.: 257

Bravo AF: 0.287

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.4
DANN	Benign	0.41
PhyloP100		-0.54
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs10974919; hg19: chr9-5021738; COSMIC: COSV67666201;