rs6850751

Positions:

• chr4-6052571-G-A
• chr4-6052571-G-C

Variant summary

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

The ENST00000409021.9(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 ENST00000409021.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.886

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
JAKMIP1	NM_001099433.2	c.1806+1479C>T		intron_variant		ENST00000409021.9	NP_001092903.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
JAKMIP1	ENST00000409021.9	c.1806+1479C>T		intron_variant		1	NM_001099433.2	ENSP00000386711	P1

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

Gnomad4 AFR AF: 0.653

Gnomad4 AMR AF: 0.161

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.00177

Gnomad4 SAS AF: 0.176

Gnomad4 FIN AF: 0.0837

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.246

Alfa AF: 0.140 Hom.: 497

Bravo AF: 0.306

Asia WGS AF: 0.132 AC: 458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.78
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6850751; hg19: chr4-6054298;