rs7084312

Positions:

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

Variant summary

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

The ENST00000657785.1(JAKMIP3):​c.-138+3046G>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 ENST00000657785.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.36

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=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
JAKMIP3	NM_001392043.1	c.-138+3376G>A		intron_variant
JAKMIP3	NM_001392044.1	c.-138+3046G>A		intron_variant
JAKMIP3	NM_001392055.1	c.-138+3376G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
JAKMIP3	ENST00000657785.1	c.-138+3046G>A		intron_variant				A2
JAKMIP3	ENST00000668452.1	c.-138+3376G>A		intron_variant				P4

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

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.0338

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.125

Alfa AF: 0.138 Hom.: 2058

Bravo AF: 0.127

Asia WGS AF: 0.0850 AC: 294 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	0.016
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7084312; hg19: chr10-133853288;