rs7664611
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
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
NM_001099433.2 intron
Scores
2
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]
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ACMG classification
Classification made for transcript
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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
JAKMIP1 | NM_001099433.2 | c.-147-7411G>A | intron_variant | ENST00000409021.9 | NP_001092903.1 | |||
JAKMIP1 | NM_001306133.2 | c.-147-7411G>A | intron_variant | NP_001293062.1 | ||||
JAKMIP1 | NM_144720.4 | c.-147-7411G>A | intron_variant | NP_653321.1 | ||||
JAKMIP1 | NM_001306134.2 | c.-147-7411G>A | intron_variant | NP_001293063.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.457 AC: 69363AN: 151872Hom.: 16020 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.456 AC: 69377AN: 151990Hom.: 16018 Cov.: 32 AF XY: 0.450 AC XY: 33390AN XY: 74270
GnomAD4 genome
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32
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1230
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3478
ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at