10-132169923-C-T

Position:

• chr10-132169923-C-T

Variant summary

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

The NM_001392041.1(JAKMIP3):​c.*1117C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 152,332 control chromosomes in the GnomAD database, including 22,527 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 0.53 (22473 hom., cov: 33)
  • Exomes 𝑓: 0.55 (54 hom.)
• Consequence: JAKMIP3 NM_001392041.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.986

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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.917 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
JAKMIP3	NM_001323087.2	c.*1103+890C>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.*1103+890C>T		intron_variant			NM_001323087.2	ENSP00000508932.1

Frequencies

GnomAD3 genomes AF: 0.529 AC: 80379 AN: 151880 Hom.: 22444 Cov.: 33

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.649

Gnomad AMR AF: 0.654

Gnomad ASJ AF: 0.536

Gnomad EAS AF: 0.939

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.545

GnomAD4 exome AF: 0.548 AC: 183 AN: 334 Hom.: 54 Cov.: 0 AF XY: 0.551 AC XY: 140 AN XY: 254

Gnomad4 AFR exome AF: 0.583

Gnomad4 AMR exome AF: 0.750

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.917

Gnomad4 SAS exome AF: 0.750

Gnomad4 FIN exome AF: 0.389

Gnomad4 NFE exome AF: 0.537

Gnomad4 OTH exome AF: 0.375

GnomAD4 genome AF: 0.529 AC: 80450 AN: 151998 Hom.: 22473 Cov.: 33 AF XY: 0.532 AC XY: 39508 AN XY: 74298

Gnomad4 AFR AF: 0.375

Gnomad4 AMR AF: 0.655

Gnomad4 ASJ AF: 0.536

Gnomad4 EAS AF: 0.939

Gnomad4 SAS AF: 0.614

Gnomad4 FIN AF: 0.495

Gnomad4 NFE AF: 0.561

Gnomad4 OTH AF: 0.547

Alfa AF: 0.517 Hom.: 2939

Bravo AF: 0.537

Asia WGS AF: 0.755 AC: 2627 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	1.5
DANN	Benign	0.59

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs7096307; hg19: chr10-133983427; COSMIC: COSV53829917;