rs954820

Variant names:

• chr10-132144257-G-A
• rs954820
• NM_001323087.2:c.1603-850G>A

Variant summary

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

The NM_001323087.2(JAKMIP3):​c.1603-850G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.681 in 152,192 control chromosomes in the GnomAD database, including 36,893 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 0.68 (36884 hom., cov: 32)
  • Exomes 𝑓: 0.44 (9 hom.)
• Consequence: JAKMIP3 NM_001323087.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.564

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.882 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
JAKMIP3	NM_001323087.2	c.1603-850G>A		intron_variant	Intron 11 of 23	ENST00000684848.1	NP_001310016.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
JAKMIP3	ENST00000684848.1	c.1603-850G>A		intron_variant	Intron 11 of 23		NM_001323087.2	ENSP00000508932.1

Frequencies

GnomAD3 genomes AF: 0.681 AC: 103524 AN: 152004 Hom.: 36827 Cov.: 32

Gnomad AFR AF: 0.889

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.655

Gnomad EAS AF: 0.770

Gnomad SAS AF: 0.735

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.678

GnomAD4 exome AF: 0.443 AC: 31 AN: 70 Hom.: 9 Cov.: 0 AF XY: 0.452 AC XY: 28 AN XY: 62

Gnomad4 AFR exome AF: 1.00

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 0.667

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.417

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.681 AC: 103643 AN: 152122 Hom.: 36884 Cov.: 32 AF XY: 0.687 AC XY: 51114 AN XY: 74350

Gnomad4 AFR AF: 0.889

Gnomad4 AMR AF: 0.696

Gnomad4 ASJ AF: 0.655

Gnomad4 EAS AF: 0.770

Gnomad4 SAS AF: 0.734

Gnomad4 FIN AF: 0.598

Gnomad4 NFE AF: 0.556

Gnomad4 OTH AF: 0.680

Alfa AF: 0.609 Hom.: 15118

Bravo AF: 0.695

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.18
DANN	Benign	0.31

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

Publications

LitVar

Other links and lift over

dbSNP: rs954820; hg19: chr10-133957761;