4-6194235-C-T

Position:

• chr4-6194235-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001099433.2(JAKMIP1):​c.-148+6018G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 151,760 control chromosomes in the GnomAD database, including 15,830 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 0.44 (15830 hom., cov: 31)
• Consequence: JAKMIP1 NM_001099433.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.27

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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.59 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
JAKMIP1	NM_001099433.2	c.-148+6018G>A		intron_variant		ENST00000409021.9
JAKMIP1	NM_001306133.2	c.-148+256G>A		intron_variant
JAKMIP1	NM_001306134.2	c.-148+256G>A		intron_variant
JAKMIP1	NM_144720.4	c.-148+6018G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
JAKMIP1	ENST00000409021.9	c.-148+6018G>A		intron_variant		1	NM_001099433.2	P1

Frequencies

GnomAD3 genomes AF: 0.439 AC: 66566 AN: 151640 Hom.: 15824 Cov.: 31

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.608

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.439 AC: 66590 AN: 151760 Hom.: 15830 Cov.: 31 AF XY: 0.442 AC XY: 32797 AN XY: 74148

Gnomad4 AFR AF: 0.243

Gnomad4 AMR AF: 0.542

Gnomad4 ASJ AF: 0.639

Gnomad4 EAS AF: 0.608

Gnomad4 SAS AF: 0.499

Gnomad4 FIN AF: 0.492

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.484

Alfa AF: 0.499 Hom.: 30857

Bravo AF: 0.438

Asia WGS AF: 0.577 AC: 2009 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.025
DANN	Benign	0.63

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: rs10470721; hg19: chr4-6195962;