rs9991241

Variant names:

• chr4-6198708-T-C
• rs9991241
• NM_001099433.2:c.-148+1545A>G

Variant summary

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

The NM_001099433.2(JAKMIP1):​c.-148+1545A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 152,192 control chromosomes in the GnomAD database, including 4,289 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 0.22 (4289 hom., cov: 33)
• Consequence: JAKMIP1 NM_001099433.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96
• Publications: 0 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.357 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	JAKMIP1	NM_001099433.2	MANE Select	c.-148+1545A>G		intron	N/A	NP_001092903.1
	JAKMIP1	NM_144720.4		c.-148+1545A>G		intron	N/A	NP_653321.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	JAKMIP1	ENST00000409021.9	TSL:1 MANE Select	c.-148+1545A>G		intron	N/A	ENSP00000386711.3
	JAKMIP1	ENST00000409371.8	TSL:1	c.-148+1545A>G		intron	N/A	ENSP00000387042.3
	JAKMIP1	ENST00000282924.9	TSL:1	c.-148+1545A>G		intron	N/A	ENSP00000282924.5

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34185 AN: 152074 Hom.: 4282 Cov.: 33

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.225 AC: 34215 AN: 152192 Hom.: 4289 Cov.: 33 AF XY: 0.227 AC XY: 16901 AN XY: 74406

African (AFR) AF: 0.303 AC: 12592 AN: 41524

American (AMR) AF: 0.220 AC: 3357 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 568 AN: 3472

East Asian (EAS) AF: 0.370 AC: 1914 AN: 5168

South Asian (SAS) AF: 0.277 AC: 1335 AN: 4812

European-Finnish (FIN) AF: 0.226 AC: 2393 AN: 10600

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.167 AC: 11384 AN: 68006

Other (OTH) AF: 0.202 AC: 426 AN: 2114

Alfa AF: 0.198 Hom.: 1196

Bravo AF: 0.228

Asia WGS AF: 0.299 AC: 1040 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.85
DANN	Benign	0.48
PhyloP100		-2.0
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: rs9991241; hg19: chr4-6200435;