rs9991241

chr4-6198708-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
JAKMIP1	NM_001099433.2	c.-148+1545A>G		intron_variant		ENST00000409021.9
JAKMIP1	NM_144720.4	c.-148+1545A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
JAKMIP1	ENST00000409021.9	c.-148+1545A>G		intron_variant		1	NM_001099433.2	P1

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

Gnomad4 AFR AF: 0.303

Gnomad4 AMR AF: 0.220

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.370

Gnomad4 SAS AF: 0.277

Gnomad4 FIN AF: 0.226

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.202

Alfa AF: 0.186 Hom.: 561

Bravo AF: 0.228

Asia WGS AF: 0.299 AC: 1040 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.85
Dann	Benign	0.48

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: rs9991241; hg19: chr4-6200435;