rs16838131

Variant names:

• chr4-6056770-G-A
• rs16838131
• NM_001099433.2:c.1645-11C>T

Variant summary

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

The NM_001099433.2(JAKMIP1):​c.1645-11C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00445 in 1,592,416 control chromosomes in the GnomAD database, including 206 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 0.022 (116 hom., cov: 33)
  • Exomes 𝑓: 0.0026 (90 hom.)
• Consequence: JAKMIP1 NM_001099433.2 intron
• Scores: Splicing: ADA: 0.00001627
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.223
• Publications: 5 publications found

Genes affected

JAKMIP1 (HGNC:26460): (janus kinase and microtubule interacting protein 1) Enables GABA receptor binding activity and RNA binding activity. Involved in cognition. Is extrinsic component of membrane. Part of ribonucleoprotein complex. [provided by Alliance of Genome Resources, Apr 2022]

C4orf50 (HGNC:33766): (chromosome 4 open reading frame 50)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0713 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001099433.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	JAKMIP1	NM_001099433.2	MANE Select	c.1645-11C>T		intron	N/A	NP_001092903.1	Q96N16-2
	JAKMIP1	NM_001306133.2		c.1645-11C>T		intron	N/A	NP_001293062.1	Q96N16-1
	JAKMIP1	NM_144720.4		c.1645-11C>T		intron	N/A	NP_653321.1	Q96N16-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	JAKMIP1	ENST00000409021.9	TSL:1 MANE Select	c.1645-11C>T		intron	N/A	ENSP00000386711.3	Q96N16-2
	JAKMIP1	ENST00000409371.8	TSL:1	c.1090-11C>T		intron	N/A	ENSP00000387042.3	Q96N16-5
	JAKMIP1	ENST00000282924.9	TSL:1	c.1645-11C>T		intron	N/A	ENSP00000282924.5	Q96N16-1

Frequencies

GnomAD3 genomes AF: 0.0215 AC: 3272 AN: 152176 Hom.: 117 Cov.: 33

Gnomad AFR AF: 0.0736

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00798

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.000808

Gnomad OTH AF: 0.0205

GnomAD2 exomes AF: 0.00598 AC: 1501 AN: 250798 AF XY: 0.00436

Gnomad AFR exome AF: 0.0735

Gnomad AMR exome AF: 0.00500

Gnomad ASJ exome AF: 0.000595

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.000143

Gnomad NFE exome AF: 0.000782

Gnomad OTH exome AF: 0.00489

GnomAD4 exome AF: 0.00264 AC: 3806 AN: 1440122 Hom.: 90 Cov.: 27 AF XY: 0.00238 AC XY: 1708 AN XY: 717944

African (AFR) AF: 0.0737 AC: 2432 AN: 33020

American (AMR) AF: 0.00539 AC: 241 AN: 44702

Ashkenazi Jewish (ASJ) AF: 0.000692 AC: 18 AN: 25998

East Asian (EAS) AF: 0.00 AC: 0 AN: 39614

South Asian (SAS) AF: 0.000221 AC: 19 AN: 85828

European-Finnish (FIN) AF: 0.0000572 AC: 3 AN: 52448

Middle Eastern (MID) AF: 0.00524 AC: 30 AN: 5728

European-Non Finnish (NFE) AF: 0.000639 AC: 699 AN: 1093142

Other (OTH) AF: 0.00610 AC: 364 AN: 59642

GnomAD4 genome AF: 0.0215 AC: 3279 AN: 152294 Hom.: 116 Cov.: 33 AF XY: 0.0202 AC XY: 1501 AN XY: 74476

African (AFR) AF: 0.0735 AC: 3054 AN: 41538

American (AMR) AF: 0.00797 AC: 122 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.000288 AC: 1 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5184

South Asian (SAS) AF: 0.000207 AC: 1 AN: 4832

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10620

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.000809 AC: 55 AN: 68020

Other (OTH) AF: 0.0203 AC: 43 AN: 2116

Alfa AF: 0.0110 Hom.: 111

Bravo AF: 0.0243

Asia WGS AF: 0.00520 AC: 18 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	16
DANN	Benign	0.60
PhyloP100		0.22
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.000016
dbscSNV1_RF	Benign	0.0
SpliceAI score (max)		0.070		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: rs16838131; hg19: chr4-6058497;