Genetic Variant JAKMIP3:c.*1103+890C>T (chr10-132169923-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001323087.2(JAKMIP3):c.*1103+890C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 152,332 control chromosomes in the GnomAD database, including 22,527 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 0.53 ( 22473 hom., cov: 33)

Exomes 𝑓: 0.55 ( 54 hom. )

Consequence

JAKMIP3
NM_001323087.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.986

Publications

10 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:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.0).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.917 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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
JAKMIP3	NM_001323087.2	MANE Select	c.*1103+890C>T	intron	N/A	NP_001310016.1
JAKMIP3	NM_001392041.1		c.*1117C>T	3_prime_UTR	Exon 24 of 25	NP_001378970.1
JAKMIP3	NM_001392042.1		c.*1310C>T	3_prime_UTR	Exon 24 of 25	NP_001378971.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
JAKMIP3	ENST00000684848.1	MANE Select	c.*1103+890C>T	intron	N/A	ENSP00000508932.1
JAKMIP3	ENST00000477275.1	TSL:1	n.2987+890C>T	intron	N/A
JAKMIP3	ENST00000666974.1		c.*1310C>T	3_prime_UTR	Exon 24 of 25	ENSP00000499416.1

Frequencies

GnomAD3 genomes

AF:

0.529

AC:

80379

AN:

151880

Hom.:

22444

Cov.:

show subpopulations

Gnomad AFR

AF:

0.375

Gnomad AMI

AF:

0.649

Gnomad AMR

AF:

0.654

Gnomad ASJ

AF:

0.536

Gnomad EAS

AF:

0.939

Gnomad SAS

AF:

0.611

Gnomad FIN

AF:

0.495

Gnomad MID

AF:

0.468

Gnomad NFE

AF:

0.561

Gnomad OTH

AF:

0.545

GnomAD4 exome

AF:

0.548

AC:

183

AN:

334

Hom.:

Cov.:

AF XY:

0.551

AC XY:

140

AN XY:

254

show subpopulations

African (AFR)

AF:

0.583

AC:

AN:

American (AMR)

AF:

0.750

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AF:

0.917

AC:

AN:

South Asian (SAS)

AF:

0.750

AC:

AN:

European-Finnish (FIN)

AF:

0.389

AC:

AN:

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.537

AC:

144

AN:

268

Other (OTH)

AF:

0.375

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.515

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.529

AC:

80450

AN:

151998

Hom.:

22473

Cov.:

AF XY:

0.532

AC XY:

39508

AN XY:

74298

show subpopulations

African (AFR)

AF:

0.375

AC:

15551

AN:

41460

American (AMR)

AF:

0.655

AC:

10009

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.536

AC:

1858

AN:

3468

East Asian (EAS)

AF:

0.939

AC:

4849

AN:

5164

South Asian (SAS)

AF:

0.614

AC:

2959

AN:

4822

European-Finnish (FIN)

AF:

0.495

AC:

5237

AN:

10576

Middle Eastern (MID)

AF:

0.469

AC:

138

AN:

294

European-Non Finnish (NFE)

AF:

0.561

AC:

38102

AN:

67906

Other (OTH)

AF:

0.547

AC:

1155

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1875

3750

5625

7500

9375

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

696

1392

2088

2784

3480

<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:

0.535

Hom.:

5835

Bravo

AF:

0.537

Asia WGS

AF:

0.755

AC:

2627

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.5

(source)

DANN

Benign

0.59

PhyloP100

-0.99

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over