rs6850751

Variant names:

• chr4-6052571-G-A
• rs6850751
• NM_001099433.2:c.1806+1479C>T

Your query was ambiguous. Multiple possible variants found:

• chr4-6052571-G-A
• chr4-6052571-G-C

Variant summary

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

The NM_001099433.2(JAKMIP1):​c.1806+1479C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 150,460 control chromosomes in the GnomAD database, including 10,090 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 0.28 (10090 hom., cov: 28)
• Consequence: JAKMIP1 NM_001099433.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.886
• 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.646 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.1806+1479C>T		intron	N/A	NP_001092903.1	Q96N16-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	JAKMIP1	ENST00000409021.9	TSL:1 MANE Select	c.1806+1479C>T		intron	N/A	ENSP00000386711.3	Q96N16-2
	JAKMIP1	ENST00000409371.8	TSL:1	c.1251+1479C>T		intron	N/A	ENSP00000387042.3	Q96N16-5
	C4orf50	ENST00000531445.3	TSL:5	c.-3141+1479C>T		intron	N/A	ENSP00000437121.2	Q6ZRC1

Frequencies

GnomAD3 genomes AF: 0.283 AC: 42510 AN: 150346 Hom.: 10048 Cov.: 28

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.00176

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.0837

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.283 AC: 42613 AN: 150460 Hom.: 10090 Cov.: 28 AF XY: 0.274 AC XY: 20135 AN XY: 73400

African (AFR) AF: 0.653 AC: 26527 AN: 40630

American (AMR) AF: 0.161 AC: 2436 AN: 15144

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 471 AN: 3462

East Asian (EAS) AF: 0.00177 AC: 9 AN: 5092

South Asian (SAS) AF: 0.176 AC: 835 AN: 4740

European-Finnish (FIN) AF: 0.0837 AC: 868 AN: 10374

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.158 AC: 10723 AN: 67732

Other (OTH) AF: 0.246 AC: 512 AN: 2082

Alfa AF: 0.161 Hom.: 662

Bravo AF: 0.306

Asia WGS AF: 0.132 AC: 458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.78
DANN	Benign	0.50
PhyloP100		-0.89
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6850751; hg19: chr4-6054298;