rs9419187

Positions:

• chr10-132098428-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001323087.2(JAKMIP3):​c.-137-6244T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.613 in 152,052 control chromosomes in the GnomAD database, including 28,786 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 0.61 (28786 hom., cov: 33)
• Consequence: JAKMIP3 NM_001323087.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
JAKMIP3	NM_001323087.2	c.-137-6244T>C		intron_variant		ENST00000684848.1	NP_001310016.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
JAKMIP3	ENST00000684848.1	c.-137-6244T>C		intron_variant			NM_001323087.2	ENSP00000508932	A2

Frequencies

GnomAD3 genomes AF: 0.613 AC: 93062 AN: 151932 Hom.: 28764 Cov.: 33

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.748

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.694

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.646

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.613 AC: 93142 AN: 152052 Hom.: 28786 Cov.: 33 AF XY: 0.617 AC XY: 45837 AN XY: 74336

Gnomad4 AFR AF: 0.524

Gnomad4 AMR AF: 0.608

Gnomad4 ASJ AF: 0.632

Gnomad4 EAS AF: 0.707

Gnomad4 SAS AF: 0.694

Gnomad4 FIN AF: 0.657

Gnomad4 NFE AF: 0.646

Gnomad4 OTH AF: 0.603

Alfa AF: 0.640 Hom.: 14189

Bravo AF: 0.603

Asia WGS AF: 0.675 AC: 2343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.021
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9419187; hg19: chr10-133911932; COSMIC: COSV56029963;