rs3790541

Positions:

• chr1-64875884-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002227.4(JAK1):​c.330-2361G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 152,058 control chromosomes in the GnomAD database, including 1,807 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 0.15 (1807 hom., cov: 32)
  • Exomes 𝑓: 0.12 (0 hom.)
• Consequence: JAK1 NM_002227.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
JAK1	NM_002227.4	c.330-2361G>A		intron_variant		ENST00000342505.5	NP_002218.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
JAK1	ENST00000342505.5	c.330-2361G>A		intron_variant		5	NM_002227.4	ENSP00000343204.4

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22716 AN: 151882 Hom.: 1804 Cov.: 32

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.0987

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.141

GnomAD4 exome AF: 0.121 AC: 7 AN: 58 Hom.: 0 AF XY: 0.118 AC XY: 4 AN XY: 34

Gnomad4 AFR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.130

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.150 AC: 22738 AN: 152000 Hom.: 1807 Cov.: 32 AF XY: 0.152 AC XY: 11298 AN XY: 74290

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.313

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.114

Gnomad4 OTH AF: 0.139

Alfa AF: 0.121 Hom.: 2500

Bravo AF: 0.155

Asia WGS AF: 0.230 AC: 799 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.4
DANN	Benign	0.83
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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

LitVar

Other links and lift over

dbSNP: rs3790541; hg19: chr1-65341567;