4-6181457-T-G

Variant names:

• chr4-6181457-T-G
• rs10937705
• NM_001099433.2:c.-148+18796A>C

Variant summary

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

The NM_001099433.2(JAKMIP1):​c.-148+18796A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.69 in 151,934 control chromosomes in the GnomAD database, including 37,637 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 0.69 (37637 hom., cov: 31)
• Consequence: JAKMIP1 NM_001099433.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.486

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)

ENSG00000287786 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.963 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
JAKMIP1	NM_001099433.2	c.-148+18796A>C		intron_variant	Intron 1 of 20	ENST00000409021.9	NP_001092903.1
JAKMIP1	NM_001306133.2	c.-148+13034A>C		intron_variant	Intron 1 of 12		NP_001293062.1
JAKMIP1	NM_144720.4	c.-148+18796A>C		intron_variant	Intron 1 of 12		NP_653321.1
JAKMIP1	NM_001306134.2	c.-148+13034A>C		intron_variant	Intron 1 of 11		NP_001293063.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
JAKMIP1	ENST00000409021.9	c.-148+18796A>C		intron_variant	Intron 1 of 20	1	NM_001099433.2	ENSP00000386711.3

Frequencies

GnomAD3 genomes AF: 0.690 AC: 104735 AN: 151816 Hom.: 37625 Cov.: 31

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.753

Gnomad AMR AF: 0.791

Gnomad ASJ AF: 0.712

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.823

Gnomad FIN AF: 0.795

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.746

Gnomad OTH AF: 0.698

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

GnomAD4 genome AF: 0.690 AC: 104772 AN: 151934 Hom.: 37637 Cov.: 31 AF XY: 0.697 AC XY: 51727 AN XY: 74250

Gnomad4 AFR AF: 0.475

Gnomad4 AMR AF: 0.791

Gnomad4 ASJ AF: 0.712

Gnomad4 EAS AF: 0.986

Gnomad4 SAS AF: 0.824

Gnomad4 FIN AF: 0.795

Gnomad4 NFE AF: 0.746

Gnomad4 OTH AF: 0.702

Alfa AF: 0.741 Hom.: 53728

Bravo AF: 0.681

Asia WGS AF: 0.865 AC: 3008 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.82

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: rs10937705; hg19: chr4-6183184;