rs4880241

Positions:

• chr10-132163594-C-T

Variant summary

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

The NM_001323087.2(JAKMIP3):​c.2424+182C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.441 in 151,938 control chromosomes in the GnomAD database, including 16,533 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 0.44 (16533 hom., cov: 33)
• Consequence: JAKMIP3 NM_001323087.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94

Genes affected

JAKMIP3 (HGNC:23523): (Janus kinase and microtubule interacting protein 3) Predicted to enable kinase binding activity and microtubule binding activity. Predicted to be located in Golgi apparatus. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
JAKMIP3	NM_001323087.2	c.2424+182C>T		intron_variant		ENST00000684848.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
JAKMIP3	ENST00000684848.1	c.2424+182C>T		intron_variant			NM_001323087.2	A2

Frequencies

GnomAD3 genomes AF: 0.441 AC: 66950 AN: 151818 Hom.: 16510 Cov.: 33

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.441 AC: 66983 AN: 151938 Hom.: 16533 Cov.: 33 AF XY: 0.440 AC XY: 32635 AN XY: 74230

Gnomad4 AFR AF: 0.217

Gnomad4 AMR AF: 0.615

Gnomad4 ASJ AF: 0.423

Gnomad4 EAS AF: 0.362

Gnomad4 SAS AF: 0.531

Gnomad4 FIN AF: 0.431

Gnomad4 NFE AF: 0.538

Gnomad4 OTH AF: 0.448

Alfa AF: 0.474 Hom.: 2349

Bravo AF: 0.444

Asia WGS AF: 0.437 AC: 1521 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.9
DANN	Benign	0.34

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: rs4880241; hg19: chr10-133977098;