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

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_001099433.2(JAKMIP1):​c.2029-3109C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00599 in 152,332 control chromosomes in the GnomAD database, including 10 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 0.0060 (10 hom., cov: 33)
• Consequence: JAKMIP1 NM_001099433.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.966
• Publications: 1 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=-0.94).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00599 (912/152332) while in subpopulation AFR AF = 0.0202 (840/41562). AF 95% confidence interval is 0.0191. There are 10 homozygotes in GnomAd4. There are 426 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 10 gene

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes AF: 0.00597 AC: 908 AN: 152214 Hom.: 10 Cov.: 33

Gnomad AFR AF: 0.0202

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00347

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0000588

Gnomad OTH AF: 0.00621

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

GnomAD4 genome AF: 0.00599 AC: 912 AN: 152332 Hom.: 10 Cov.: 33 AF XY: 0.00572 AC XY: 426 AN XY: 74490

African (AFR) AF: 0.0202 AC: 840 AN: 41562

American (AMR) AF: 0.00346 AC: 53 AN: 15312

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5188

South Asian (SAS) AF: 0.00 AC: 0 AN: 4824

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10622

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0000588 AC: 4 AN: 68034

Other (OTH) AF: 0.00615 AC: 13 AN: 2114

Alfa AF: 0.00185 Hom.: 0

Bravo AF: 0.00718

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.66
DANN	Benign	0.82
PhyloP100		-0.97
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs11935825; hg19: chr4-6047063;