Genetic Variant NM_001323087.2:c.136-6064C>G (chr10-132111013-C-G) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is The variant received -4 classification points (ACGS-UK Somatic Oncogenicity v2025). B1_Strong

The NM_001323087.2(JAKMIP3):c.136-6064C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a cumulative frequency of 0.233 (AC=35,509) in the gnomAD database across 152,258 control chromosomes, including 4,370 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.311. In-silico predictor (BayesDel (noAF)) classifies this variant as likely benign. Splicing prediction tools (SpliceAI) predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.23 ( 4370 hom., cov: 34)

Consequence

JAKMIP3
NM_001323087.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.329

Publications

1 publications found

Variant links:

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]

JAKMIP3 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_001323087.2, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

Classification according to ACGS-UK Somatic Oncogenicity v2025

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 points.

GnomAD effective popmax AF >1% — B1 stand-alone benign; GnomAD effective popmax AF = 0.311 — exceeds 1% threshold (B1 applied)

Variant Effect in Transcripts

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

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
JAKMIP3	NM_001323087.2	MANE Select	c.136-6064C>G	intron	N/A	NP_001310016.1	A0A590UJH1
JAKMIP3	NM_001323086.2		c.136-6064C>G	intron	N/A	NP_001310015.1	A0A590UIU4
JAKMIP3	NM_001392039.1		c.136-6064C>G	intron	N/A	NP_001378968.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
JAKMIP3	ENST00000684848.1	MANE Select	c.136-6064C>G	intron	N/A	ENSP00000508932.1	A0A590UJH1
JAKMIP3	ENST00000666210.1		c.136-6064C>G	intron	N/A	ENSP00000499222.1	A0A590UIU4
JAKMIP3	ENST00000657785.1		c.136-6064C>G	intron	N/A	ENSP00000499291.1	A0A590UJH1

Frequencies

GnomAD3 genomes

AF:

0.233

AC:

35471

AN:

152140

Hom.:

4366

Cov.:

show subpopulations

Gnomad AFR

AF:

0.316

Gnomad AMI

AF:

0.255

Gnomad AMR

AF:

0.153

Gnomad ASJ

AF:

0.153

Gnomad EAS

AF:

0.287

Gnomad SAS

AF:

0.249

Gnomad FIN

AF:

0.165

Gnomad MID

AF:

0.187

Gnomad NFE

AF:

0.210

Gnomad OTH

AF:

0.234

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

GnomAD4 genome

AF:

0.233

AC:

35509

AN:

152258

Hom.:

4370

Cov.:

AF XY:

0.231

AC XY:

17204

AN XY:

74442

show subpopulations

African (AFR)

AF:

0.316

AC:

13113

AN:

41522

American (AMR)

AF:

0.153

AC:

2342

AN:

15310

Ashkenazi Jewish (ASJ)

AF:

0.153

AC:

532

AN:

3472

East Asian (EAS)

AF:

0.287

AC:

1482

AN:

5164

South Asian (SAS)

AF:

0.248

AC:

1199

AN:

4834

European-Finnish (FIN)

AF:

0.165

AC:

1748

AN:

10612

Middle Eastern (MID)

AF:

0.194

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.210

AC:

14308

AN:

68022

Other (OTH)

AF:

0.234

AC:

495

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1459

2919

4378

5838

7297

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

376

752

1128

1504

1880

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.126

Hom.:

214

Bravo

AF:

0.235

Asia WGS

AF:

0.228

AC:

790

AN:

3478

Local populations

ToMMo 61KJPN (+60KJPN MNV)

AF:

0.322

AC:

39506

AN:

122790

Turkish Variome

AF:

0.205

AC:

317

AN:

1546

Hom.:

WBBC (Westlake BioBank for Chinese) pilot

AF:

0.300

AC:

2692

AN:

8960

Hom.:

400

ABraOM SABE-WGS-1171

AF:

0.222

AC:

521

AN:

2342

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

1.3

(source)

DANN

Benign

0.60

PhyloP100

-0.33

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

Classification according to ACGS-UK Somatic Oncogenicity v2025

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Local populations

ClinVar

Computational scores

Splicing

Publications

Other links and lift over