NM_001323087.2:c.-138+6764G>A

Variant names:

• chr10-132072825-G-A
• rs11819434
• NM_001323087.2:c.-138+6764G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 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=-0.97).
• 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 rank	MANE	Protein	UniProt
JAKMIP3	NM_001323087.2	c.-138+6764G>A		intron_variant	Intron 1 of 23	ENST00000684848.1	NP_001310016.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
JAKMIP3	ENST00000684848.1	c.-138+6764G>A		intron_variant	Intron 1 of 23		NM_001323087.2	ENSP00000508932.1

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

African (AFR) AF: 0.451 AC: 18564 AN: 41180

American (AMR) AF: 0.564 AC: 8601 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.361 AC: 1247 AN: 3458

East Asian (EAS) AF: 0.426 AC: 2183 AN: 5124

South Asian (SAS) AF: 0.395 AC: 1894 AN: 4798

European-Finnish (FIN) AF: 0.449 AC: 4681 AN: 10428

Middle Eastern (MID) AF: 0.438 AC: 128 AN: 292

European-Non Finnish (NFE) AF: 0.369 AC: 24995 AN: 67808

Other (OTH) AF: 0.416 AC: 876 AN: 2106

Alfa AF: 0.382 Hom.: 4216

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
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs11819434; hg19: chr10-133886329;