NM_001099433.2:c.2029-3109C>T

Variant names:

• chr4-6045336-G-A
• rs11935825
• NM_001099433.2:c.2029-3109C>T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001099433.2(JAKMIP1):​c.2029-3109C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00257 in 152,336 control chromosomes in the GnomAD database, including 1 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 0.0026 (1 hom., cov: 33)
• Consequence: JAKMIP1 NM_001099433.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.966

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 Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
JAKMIP1	NM_001099433.2	c.2029-3109C>T		intron_variant	Intron 16 of 20	ENST00000409021.9	NP_001092903.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
JAKMIP1	ENST00000409021.9	c.2029-3109C>T		intron_variant	Intron 16 of 20	1	NM_001099433.2	ENSP00000386711.3
JAKMIP1	ENST00000409371.8	c.1474-3109C>T		intron_variant	Intron 14 of 18	1		ENSP00000387042.3
C4orf50	ENST00000531445.3	c.-2918-3109C>T		intron_variant	Intron 16 of 33	5		ENSP00000437121.2
JAKMIP1	ENST00000637373.2	c.733-3109C>T		intron_variant	Intron 9 of 13	5		ENSP00000490067.1

Frequencies

GnomAD3 genomes AF: 0.00254 AC: 387 AN: 152218 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.00820

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00105

Gnomad ASJ AF: 0.00288

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.000206

Gnomad OTH AF: 0.00287

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

GnomAD4 genome AF: 0.00257 AC: 391 AN: 152336 Hom.: 1 Cov.: 33 AF XY: 0.00248 AC XY: 185 AN XY: 74488

Gnomad4 AFR AF: 0.00828

Gnomad4 AMR AF: 0.00104

Gnomad4 ASJ AF: 0.00288

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000206

Gnomad4 OTH AF: 0.00284

Bravo AF: 0.00280

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.79
DANN	Benign	0.97

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11935825; hg19: chr4-6047063;