10-132157084-C-T

Position:

• chr10-132157084-C-T

Variant summary

Our verdict is Benign. Variant got -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

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
JAKMIP3	NM_001323087.2	c.2220+3094C>T		intron_variant		ENST00000684848.1	NP_001310016.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
JAKMIP3	ENST00000684848.1	c.2220+3094C>T		intron_variant			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

Gnomad4 AFR AF: 0.354

Gnomad4 AMR AF: 0.613

Gnomad4 ASJ AF: 0.533

Gnomad4 EAS AF: 0.388

Gnomad4 SAS AF: 0.429

Gnomad4 FIN AF: 0.493

Gnomad4 NFE AF: 0.624

Gnomad4 OTH AF: 0.522

Alfa AF: 0.603 Hom.: 40807

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

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

LitVar

Other links and lift over

dbSNP: rs870552; hg19: chr10-133970588;