rs4880241

Variant names:

• chr10-132163594-C-T
• rs4880241
• NM_001323087.2:c.2424+182C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001323087.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	JAKMIP3	NM_001323087.2	MANE Select	c.2424+182C>T		intron	N/A	NP_001310016.1
	JAKMIP3	NM_001323086.2		c.2424+182C>T		intron	N/A	NP_001310015.1
	JAKMIP3	NM_001392039.1		c.2472+182C>T		intron	N/A	NP_001378968.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	JAKMIP3	ENST00000684848.1	MANE Select	c.2424+182C>T		intron	N/A	ENSP00000508932.1
	JAKMIP3	ENST00000477275.1	TSL:1	n.1798+182C>T		intron	N/A
	JAKMIP3	ENST00000666210.1		c.2424+182C>T		intron	N/A	ENSP00000499222.1

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

African (AFR) AF: 0.217 AC: 8984 AN: 41422

American (AMR) AF: 0.615 AC: 9412 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.423 AC: 1467 AN: 3472

East Asian (EAS) AF: 0.362 AC: 1848 AN: 5104

South Asian (SAS) AF: 0.531 AC: 2554 AN: 4812

European-Finnish (FIN) AF: 0.431 AC: 4557 AN: 10580

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.538 AC: 36524 AN: 67938

Other (OTH) AF: 0.448 AC: 947 AN: 2112

Alfa AF: 0.377 Hom.: 2888

Bravo AF: 0.444

Asia WGS AF: 0.437 AC: 1521 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.9
DANN	Benign	0.34
PhyloP100		-1.9
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: rs4880241; hg19: chr10-133977098;