rs11819434

chr10-132072825-G-Achr10-132072825-G-C

Variant summary

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

The NM_001323087.2(JAKMIP3):c.-138+6764G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 151,342 control chromosomes in the GnomAD database, including 13,521 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 0.42 (13521 hom., cov: 30)
• Consequence: JAKMIP3 NM_001323087.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171

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=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
JAKMIP3	NM_001323087.2	c.-138+6764G>A		intron_variant		ENST00000684848.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
JAKMIP3	ENST00000684848.1	c.-138+6764G>A		intron_variant			NM_001323087.2	A2

Frequencies

GnomAD3 genomes AF: 0.419 AC: 63431 AN: 151224 Hom.: 13502 Cov.: 30

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.427

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.419 AC: 63481 AN: 151342 Hom.: 13521 Cov.: 30 AF XY: 0.425 AC XY: 31405 AN XY: 73918

Gnomad4 AFR AF: 0.451

Gnomad4 AMR AF: 0.564

Gnomad4 ASJ AF: 0.361

Gnomad4 EAS AF: 0.426

Gnomad4 SAS AF: 0.395

Gnomad4 FIN AF: 0.449

Gnomad4 NFE AF: 0.369

Gnomad4 OTH AF: 0.416

Alfa AF: 0.381 Hom.: 3734

Bravo AF: 0.436

Asia WGS AF: 0.418 AC: 1456 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	1.5
Dann	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11819434; hg19: chr10-133886329;