rs7084312

Variant names:

• chr10-132039784-G-A
• rs7084312
• ENST00000657785.1:c.-138+3046G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-132039784-G-A
• chr10-132039784-G-C
• chr10-132039784-G-T

Variant summary

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

The NM_001392043.1(JAKMIP3):​c.-138+3376G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 152,218 control chromosomes in the GnomAD database, including 1,345 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 0.13 (1345 hom., cov: 32)
• Consequence: JAKMIP3 NM_001392043.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.36
• Publications: 1 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]

ENSG00000304740 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001392043.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	JAKMIP3	NM_001392043.1		c.-138+3376G>A		intron	N/A	NP_001378972.1	Q5VZ66
	JAKMIP3	NM_001392044.1		c.-138+3046G>A		intron	N/A	NP_001378973.1	Q5VZ66
	JAKMIP3	NM_001392055.1		c.-138+3376G>A		intron	N/A	NP_001378984.1	A0A590UK98

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	JAKMIP3	ENST00000657785.1		c.-138+3046G>A		intron	N/A	ENSP00000499291.1	A0A590UJH1
	JAKMIP3	ENST00000668452.1		c.-138+3376G>A		intron	N/A	ENSP00000499753.1	Q5VZ66
	ENSG00000304740	ENST00000805903.1		n.333-446G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19503 AN: 152100 Hom.: 1342 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.0336

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.128 AC: 19524 AN: 152218 Hom.: 1345 Cov.: 32 AF XY: 0.124 AC XY: 9251 AN XY: 74412

African (AFR) AF: 0.113 AC: 4682 AN: 41546

American (AMR) AF: 0.107 AC: 1632 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 608 AN: 3468

East Asian (EAS) AF: 0.0338 AC: 175 AN: 5172

South Asian (SAS) AF: 0.119 AC: 576 AN: 4828

European-Finnish (FIN) AF: 0.112 AC: 1186 AN: 10598

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10099 AN: 67984

Other (OTH) AF: 0.125 AC: 263 AN: 2108

Alfa AF: 0.137 Hom.: 2529

Bravo AF: 0.127

Asia WGS AF: 0.0850 AC: 294 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.016
DANN	Benign	0.59
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs7084312; hg19: chr10-133853288;