Genetic Variant NM_144570.3:c.41C>T (chr16-1678353-C-T) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_144570.3(JPT2):c.41C>T(p.Ser14Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000926 in 1,080,458 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S14C) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 9.3e-7 ( 0 hom. )

Consequence

JPT2
NM_144570.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.56

Publications

0 publications found

Variant links:

Genes affected

JPT2 (HGNC:14137): (Jupiter microtubule associated homolog 2) Located in cytosol and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

JPT2 links:

ENSG00000261732 (HGNC:):

ENSG00000261732 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.22171855).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_144570.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
JPT2	NM_144570.3	MANE Select	c.41C>T	p.Ser14Phe	missense	Exon 1 of 5	NP_653171.1	Q9H910-1
JPT2	NM_001434664.1		c.41C>T	p.Ser14Phe	missense	Exon 1 of 7	NP_001421593.1
JPT2	NM_001434665.1		c.41C>T	p.Ser14Phe	missense	Exon 1 of 6	NP_001421594.1	Q9H910-3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
JPT2	ENST00000248098.8	TSL:1 MANE Select	c.41C>T	p.Ser14Phe	missense	Exon 1 of 5	ENSP00000248098.3	Q9H910-1
JPT2	ENST00000561516.5	TSL:1	c.41C>T	p.Ser14Phe	missense	Exon 1 of 4	ENSP00000454459.1	H3BMM8
JPT2	ENST00000569256.5	TSL:1	n.98C>T		non_coding_transcript_exon	Exon 1 of 4

Frequencies

GnomAD3 genomes

Cov.:

GnomAD2 exomes

AF:

0.00

AC:

AN:

4180

AF XY:

0.00

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

9.26e-7

AC:

AN:

1080458

Hom.:

Cov.:

AF XY:

0.00000196

AC XY:

AN XY:

510492

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

22736

American (AMR)

AF:

0.00

AC:

AN:

8416

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

14182

East Asian (EAS)

AF:

0.00

AC:

AN:

26310

South Asian (SAS)

AF:

0.00

AC:

AN:

19558

European-Finnish (FIN)

AF:

0.00

AC:

AN:

24428

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3182

European-Non Finnish (NFE)

AF:

0.00000109

AC:

AN:

918214

Other (OTH)

AF:

0.00

AC:

AN:

43432

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

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

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.20

BayesDel_addAF

Uncertain

0.030

BayesDel_noAF

Benign

-0.19

CADD

Benign

(source)

DANN

Benign

0.92

DEOGEN2

Benign

0.16

Eigen

Benign

-0.17

Eigen_PC

Benign

-0.16

FATHMM_MKL

Uncertain

0.84

LIST_S2

Benign

0.65

M_CAP

Pathogenic

0.43

MetaRNN

Benign

0.22

MetaSVM

Benign

-0.82

PhyloP100

1.6

PrimateAI

Uncertain

0.65

PROVEAN

Pathogenic

-4.4

REVEL

Benign

0.16

Sift

Benign

0.042

Sift4G

Uncertain

0.021

Polyphen

0.013

Vest4

0.26

MutPred

0.21

Loss of disorder (P = 0.0101)

MVP

0.10

MPC

0.56

ClinPred

0.97

GERP RS

3.4

PromoterAI

0.13

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.35

gMVP

0.45

Mutation Taster

=46/54

disease causing

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over