16-1678326-C-G

Variant names:

• chr16-1678326-C-G
• rs777033509
• NM_144570.3:c.14C>G

Variant summary

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

The NM_144570.3(JPT2):​c.14C>G​(p.Pro5Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000501 in 1,236,584 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P5Q) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.00026 (0 hom., cov: 32)
  • Exomes 𝑓: 0.000020 (0 hom.)
• Consequence: JPT2 NM_144570.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 1.02
• Publications: 0 publications found

Genes affected

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

ENSG00000261732 (HGNC:):

ACMG classification

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

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	JPT2	NM_144570.3	MANE Select	c.14C>G	p.Pro5Arg	missense	Exon 1 of 5	NP_653171.1	Q9H910-1
	JPT2	NM_001434664.1		c.14C>G	p.Pro5Arg	missense	Exon 1 of 7	NP_001421593.1
	JPT2	NM_001434665.1		c.14C>G	p.Pro5Arg	missense	Exon 1 of 6	NP_001421594.1	Q9H910-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	JPT2	ENST00000248098.8	TSL:1 MANE Select	c.14C>G	p.Pro5Arg	missense	Exon 1 of 5	ENSP00000248098.3	Q9H910-1
	JPT2	ENST00000561516.5	TSL:1	c.14C>G	p.Pro5Arg	missense	Exon 1 of 4	ENSP00000454459.1	H3BMM8
	JPT2	ENST00000569256.5	TSL:1	n.71C>G		non_coding_transcript_exon	Exon 1 of 4

Frequencies

GnomAD3 genomes AF: 0.000244 AC: 37 AN: 151836 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000677

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000197

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000589

Gnomad OTH AF: 0.000480

GnomAD2 exomes AF: 0.00 AC: 0 AN: 8586 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: 0.0000203 AC: 22 AN: 1084640 Hom.: 0 Cov.: 32 AF XY: 0.0000195 AC XY: 10 AN XY: 512746

African (AFR) AF: 0.000308 AC: 7 AN: 22760

American (AMR) AF: 0.00 AC: 0 AN: 8796

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14190

East Asian (EAS) AF: 0.00 AC: 0 AN: 26312

South Asian (SAS) AF: 0.0000508 AC: 1 AN: 19682

European-Finnish (FIN) AF: 0.000114 AC: 3 AN: 26360

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3634

European-Non Finnish (NFE) AF: 0.0000120 AC: 11 AN: 919380

Other (OTH) AF: 0.00 AC: 0 AN: 43526

GnomAD4 genome AF: 0.000263 AC: 40 AN: 151944 Hom.: 0 Cov.: 32 AF XY: 0.000269 AC XY: 20 AN XY: 74278

African (AFR) AF: 0.000747 AC: 31 AN: 41492

American (AMR) AF: 0.000197 AC: 3 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5148

South Asian (SAS) AF: 0.000208 AC: 1 AN: 4816

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10546

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 292

European-Non Finnish (NFE) AF: 0.0000589 AC: 4 AN: 67898

Other (OTH) AF: 0.000475 AC: 1 AN: 2106

Alfa AF: 0.000162 Hom.: 0

Bravo AF: 0.000208

ExAC AF: 0.0000764 AC: 6

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.084
BayesDel_addAF	Benign	-0.40	T
BayesDel_noAF	Benign	-0.42
CADD	Benign	13
DANN	Uncertain	0.99
DEOGEN2	Benign	0.033	T
Eigen	Benign	-0.34
Eigen_PC	Benign	-0.57
FATHMM_MKL	Benign	0.36	N
LIST_S2	Benign	0.36	T
M_CAP	Uncertain	0.21	D
MetaRNN	Benign	0.15	T
MetaSVM	Benign	-0.95	T
PhyloP100		1.0
PrimateAI	Uncertain	0.64	T
PROVEAN	Benign	-1.9	N
REVEL	Benign	0.039
Sift	Benign	0.031	D
Sift4G	Uncertain	0.035	D
Polyphen		0.73	P
Vest4		0.18
MutPred		0.33		Gain of MoRF binding (P = 9e-04)
MVP		0.082
MPC		0.80
ClinPred		0.61	D
GERP RS		-0.047
PromoterAI		-0.13	Neutral
Varity_R		0.081
gMVP		0.22
Mutation Taster		=94/6	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.43		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.43		Position offset: -5

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

Other links and lift over

dbSNP: rs777033509; hg19: chr16-1728327;