Genetic Variant JAKMIP3:c.1603-850G>A (chr10-132144257-G-A) – 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.1603-850G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.681 in 152,192 control chromosomes in the GnomAD database, including 36,893 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 0.68 ( 36884 hom., cov: 32)

Exomes 𝑓: 0.44 ( 9 hom. )

Consequence

JAKMIP3
NM_001323087.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.564

Publications

9 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=-0.94).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.882 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	UniProt
JAKMIP3	NM_001323087.2	MANE Select	c.1603-850G>A	intron	N/A	NP_001310016.1	A0A590UJH1
JAKMIP3	NM_001323086.2		c.1603-850G>A	intron	N/A	NP_001310015.1	A0A590UIU4
JAKMIP3	NM_001392039.1		c.1597-850G>A	intron	N/A	NP_001378968.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
JAKMIP3	ENST00000684848.1	MANE Select	c.1603-850G>A	intron	N/A	ENSP00000508932.1	A0A590UJH1
JAKMIP3	ENST00000477275.1	TSL:1	n.542G>A	non_coding_transcript_exon	Exon 1 of 14
JAKMIP3	ENST00000666210.1		c.1603-850G>A	intron	N/A	ENSP00000499222.1	A0A590UIU4

Frequencies

GnomAD3 genomes

AF:

0.681

AC:

103524

AN:

152004

Hom.:

36827

Cov.:

show subpopulations

Gnomad AFR

AF:

0.889

Gnomad AMI

AF:

0.592

Gnomad AMR

AF:

0.695

Gnomad ASJ

AF:

0.655

Gnomad EAS

AF:

0.770

Gnomad SAS

AF:

0.735

Gnomad FIN

AF:

0.598

Gnomad MID

AF:

0.617

Gnomad NFE

AF:

0.556

Gnomad OTH

AF:

0.678

GnomAD4 exome

AF:

0.443

AC:

AN:

Hom.:

Cov.:

AF XY:

0.452

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AF:

0.667

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.417

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.487

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Hom

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:

0.681

AC:

103643

AN:

152122

Hom.:

36884

Cov.:

AF XY:

0.687

AC XY:

51114

AN XY:

74350

show subpopulations

African (AFR)

AF:

0.889

AC:

36919

AN:

41522

American (AMR)

AF:

0.696

AC:

10641

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.655

AC:

2269

AN:

3466

East Asian (EAS)

AF:

0.770

AC:

3974

AN:

5160

South Asian (SAS)

AF:

0.734

AC:

3533

AN:

4814

European-Finnish (FIN)

AF:

0.598

AC:

6328

AN:

10584

Middle Eastern (MID)

AF:

0.626

AC:

184

AN:

294

European-Non Finnish (NFE)

AF:

0.556

AC:

37822

AN:

67972

Other (OTH)

AF:

0.680

AC:

1434

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1552

3104

4655

6207

7759

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

800

1600

2400

3200

4000

<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:

0.619

Hom.:

23004

Bravo

AF:

0.695

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.18

(source)

DANN

Benign

0.31

PhyloP100

-0.56

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

Publications

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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