NM_001099433.2:c.-148+6018G>A

Variant names:

• chr4-6194235-C-T
• rs10470721
• NM_001099433.2:c.-148+6018G>A

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+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
• Publications: 2 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.59 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+6018G>A		intron	N/A	NP_001092903.1
	JAKMIP1	NM_001306133.2		c.-148+256G>A		intron	N/A	NP_001293062.1
	JAKMIP1	NM_144720.4		c.-148+6018G>A		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+6018G>A		intron	N/A	ENSP00000386711.3
	JAKMIP1	ENST00000409371.8	TSL:1	c.-148+6018G>A		intron	N/A	ENSP00000387042.3
	JAKMIP1	ENST00000282924.9	TSL:1	c.-148+6018G>A		intron	N/A	ENSP00000282924.5

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

African (AFR) AF: 0.243 AC: 10031 AN: 41364

American (AMR) AF: 0.542 AC: 8259 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.639 AC: 2217 AN: 3468

East Asian (EAS) AF: 0.608 AC: 3120 AN: 5132

South Asian (SAS) AF: 0.499 AC: 2395 AN: 4796

European-Finnish (FIN) AF: 0.492 AC: 5165 AN: 10504

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.497 AC: 33742 AN: 67932

Other (OTH) AF: 0.484 AC: 1020 AN: 2108

Alfa AF: 0.486 Hom.: 69023

Bravo AF: 0.438

Asia WGS AF: 0.577 AC: 2009 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.025
DANN	Benign	0.63
PhyloP100		-2.3
PromoterAI		-0.021	Neutral
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: rs10470721; hg19: chr4-6195962;