rs954820

Variant names:

• chr10-132144257-G-A
• rs954820
• ENST00000477275.1:n.542G>A

Variant summary

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

The ENST00000477275.1(JAKMIP3):​n.542G>A variant causes a non coding transcript exon 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 ENST00000477275.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.564
• Publications: 9 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=-0.94).
• 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

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.500 AC: 1 AN: 2

South Asian (SAS) AF: 0.667 AC: 4 AN: 6

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.417 AC: 20 AN: 48

Other (OTH) AF: 0.500 AC: 4 AN: 8

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

African (AFR) AF: 0.889 AC: 36919 AN: 41522

American (AMR) AF: 0.696 AC: 10641 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.655 AC: 2269 AN: 3466

East Asian (EAS) AF: 0.770 AC: 3974 AN: 5160

South Asian (SAS) AF: 0.734 AC: 3533 AN: 4814

European-Finnish (FIN) AF: 0.598 AC: 6328 AN: 10584

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.556 AC: 37822 AN: 67972

Other (OTH) AF: 0.680 AC: 1434 AN: 2108

Alfa AF: 0.619 Hom.: 23004

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
PhyloP100		-0.56
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: rs954820; hg19: chr10-133957761;