rs7664611

Positions:

• chr4-6120408-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.-147-7411G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.456 in 151,990 control chromosomes in the GnomAD database, including 16,018 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 0.46 (16018 hom., cov: 32)
• Consequence: JAKMIP1 NM_001099433.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53

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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
JAKMIP1	NM_001099433.2	c.-147-7411G>A		intron_variant		ENST00000409021.9
JAKMIP1	NM_001306133.2	c.-147-7411G>A		intron_variant
JAKMIP1	NM_001306134.2	c.-147-7411G>A		intron_variant
JAKMIP1	NM_144720.4	c.-147-7411G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
JAKMIP1	ENST00000409021.9	c.-147-7411G>A		intron_variant		1	NM_001099433.2	P1

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69363 AN: 151872 Hom.: 16020 Cov.: 32

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.456 AC: 69377 AN: 151990 Hom.: 16018 Cov.: 32 AF XY: 0.450 AC XY: 33390 AN XY: 74270

Gnomad4 AFR AF: 0.421

Gnomad4 AMR AF: 0.396

Gnomad4 ASJ AF: 0.400

Gnomad4 EAS AF: 0.363

Gnomad4 SAS AF: 0.359

Gnomad4 FIN AF: 0.473

Gnomad4 NFE AF: 0.507

Gnomad4 OTH AF: 0.435

Alfa AF: 0.482 Hom.: 18425

Bravo AF: 0.451

Asia WGS AF: 0.354 AC: 1230 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.43
DANN	Benign	0.44

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: rs7664611; hg19: chr4-6122135;