10-132111013-C-G

Variant names:

• chr10-132111013-C-G
• rs2001813
• NM_001323087.2:c.136-6064C>G

Variant summary

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

The NM_001323087.2(JAKMIP3):​c.136-6064C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 152,258 control chromosomes in the GnomAD database, including 4,370 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 0.23 (4370 hom., cov: 34)
• Consequence: JAKMIP3 NM_001323087.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.329
• 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
JAKMIP3	NM_001323087.2	c.136-6064C>G		intron_variant	Intron 2 of 23	ENST00000684848.1	NP_001310016.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
JAKMIP3	ENST00000684848.1	c.136-6064C>G		intron_variant	Intron 2 of 23		NM_001323087.2	ENSP00000508932.1

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35471 AN: 152140 Hom.: 4366 Cov.: 34

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.233 AC: 35509 AN: 152258 Hom.: 4370 Cov.: 34 AF XY: 0.231 AC XY: 17204 AN XY: 74442

African (AFR) AF: 0.316 AC: 13113 AN: 41522

American (AMR) AF: 0.153 AC: 2342 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 532 AN: 3472

East Asian (EAS) AF: 0.287 AC: 1482 AN: 5164

South Asian (SAS) AF: 0.248 AC: 1199 AN: 4834

European-Finnish (FIN) AF: 0.165 AC: 1748 AN: 10612

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.210 AC: 14308 AN: 68022

Other (OTH) AF: 0.234 AC: 495 AN: 2116

Alfa AF: 0.126 Hom.: 214

Bravo AF: 0.235

Asia WGS AF: 0.228 AC: 790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.3
DANN	Benign	0.60
PhyloP100		-0.33
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2001813; hg19: chr10-133924517;