chr10-132130296-A-G

Variant names:

• chr10-132130296-A-G
• rs902633
• NM_001323087.2:c.634-3016A>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.634-3016A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.923 in 152,282 control chromosomes in the GnomAD database, including 64,971 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 0.92 (64971 hom., cov: 33)
• Consequence: JAKMIP3 NM_001323087.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.195

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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
JAKMIP3	NM_001323087.2	c.634-3016A>G		intron_variant	Intron 3 of 23	ENST00000684848.1	NP_001310016.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
JAKMIP3	ENST00000684848.1	c.634-3016A>G		intron_variant	Intron 3 of 23		NM_001323087.2	ENSP00000508932.1

Frequencies

GnomAD3 genomes AF: 0.923 AC: 140393 AN: 152164 Hom.: 64904 Cov.: 33

Gnomad AFR AF: 0.982

Gnomad AMI AF: 0.985

Gnomad AMR AF: 0.918

Gnomad ASJ AF: 0.921

Gnomad EAS AF: 0.988

Gnomad SAS AF: 0.895

Gnomad FIN AF: 0.869

Gnomad MID AF: 0.869

Gnomad NFE AF: 0.892

Gnomad OTH AF: 0.919

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

GnomAD4 genome AF: 0.923 AC: 140519 AN: 152282 Hom.: 64971 Cov.: 33 AF XY: 0.922 AC XY: 68658 AN XY: 74438

African (AFR) AF: 0.982 AC: 40814 AN: 41560

American (AMR) AF: 0.918 AC: 14052 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.921 AC: 3199 AN: 3472

East Asian (EAS) AF: 0.988 AC: 5121 AN: 5182

South Asian (SAS) AF: 0.896 AC: 4325 AN: 4826

European-Finnish (FIN) AF: 0.869 AC: 9203 AN: 10596

Middle Eastern (MID) AF: 0.877 AC: 256 AN: 292

European-Non Finnish (NFE) AF: 0.892 AC: 60704 AN: 68026

Other (OTH) AF: 0.920 AC: 1947 AN: 2116

Alfa AF: 0.901 Hom.: 105483

Bravo AF: 0.931

Asia WGS AF: 0.943 AC: 3281 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	0.77
DANN	Benign	0.44
PhyloP100		-0.20
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

Publications

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Other links and lift over

dbSNP: rs902633; hg19: chr10-133943800;