rs11935825
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_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
NM_001099433.2 intron
Scores
2
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]
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ACMG classification
Classification made for transcript
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
JAKMIP1 | NM_001099433.2 | c.2029-3109C>T | intron_variant | ENST00000409021.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
JAKMIP1 | ENST00000409021.9 | c.2029-3109C>T | intron_variant | 1 | NM_001099433.2 | P1 | |||
JAKMIP1 | ENST00000409371.8 | c.1474-3109C>T | intron_variant | 1 | |||||
C4orf50 | ENST00000531445.3 | c.-2918-3109C>T | intron_variant | 5 | P1 | ||||
JAKMIP1 | ENST00000637373.2 | c.733-3109C>T | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00254 AC: 387AN: 152218Hom.: 0 Cov.: 33
GnomAD3 genomes
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387
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.00257 AC: 391AN: 152336Hom.: 1 Cov.: 33 AF XY: 0.00248 AC XY: 185AN XY: 74488
GnomAD4 genome
?
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AC:
391
AN:
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33
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185
AN XY:
74488
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at