10-132157084-C-T

Variant names:

• chr10-132157084-C-T
• rs870552
• NM_001323087.2:c.2220+3094C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001323087.2(JAKMIP3):​c.2220+3094C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.523 in 151,866 control chromosomes in the GnomAD database, including 21,974 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 0.52 (21974 hom., cov: 31)
• Consequence: JAKMIP3 NM_001323087.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48
• Publications: 11 publications found

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]

ENSG00000305036 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
JAKMIP3	NM_001323087.2	c.2220+3094C>T		intron_variant	Intron 19 of 23	ENST00000684848.1	NP_001310016.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
JAKMIP3	ENST00000684848.1	c.2220+3094C>T		intron_variant	Intron 19 of 23		NM_001323087.2	ENSP00000508932.1

Frequencies

GnomAD3 genomes AF: 0.523 AC: 79377 AN: 151748 Hom.: 21962 Cov.: 31

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.523 AC: 79414 AN: 151866 Hom.: 21974 Cov.: 31 AF XY: 0.519 AC XY: 38499 AN XY: 74222

African (AFR) AF: 0.354 AC: 14665 AN: 41380

American (AMR) AF: 0.613 AC: 9369 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.533 AC: 1852 AN: 3472

East Asian (EAS) AF: 0.388 AC: 1997 AN: 5146

South Asian (SAS) AF: 0.429 AC: 2061 AN: 4804

European-Finnish (FIN) AF: 0.493 AC: 5207 AN: 10562

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.624 AC: 42418 AN: 67928

Other (OTH) AF: 0.522 AC: 1098 AN: 2102

Alfa AF: 0.598 Hom.: 55167

Bravo AF: 0.527

Asia WGS AF: 0.367 AC: 1277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.38
DANN	Benign	0.81
PhyloP100		-1.5
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs870552; hg19: chr10-133970588;