rs16838131

Positions:

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001099433.2(JAKMIP1):​c.1645-11C>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00445 in 1,592,416 control chromosomes in the GnomAD database, including 206 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 0.022 ( 116 hom., cov: 33)
Exomes 𝑓: 0.0026 ( 90 hom. )

Consequence

JAKMIP1
NM_001099433.2 splice_polypyrimidine_tract, intron

Scores

2
Splicing: ADA: 0.00001627
2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.223
Variant links:
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)

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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=-0.72).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0713 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
JAKMIP1NM_001099433.2 linkuse as main transcriptc.1645-11C>T splice_polypyrimidine_tract_variant, intron_variant ENST00000409021.9 NP_001092903.1
JAKMIP1NM_001306133.2 linkuse as main transcriptc.1645-11C>T splice_polypyrimidine_tract_variant, intron_variant NP_001293062.1
JAKMIP1NM_001306134.2 linkuse as main transcriptc.1150-11C>T splice_polypyrimidine_tract_variant, intron_variant NP_001293063.1
JAKMIP1NM_144720.4 linkuse as main transcriptc.1645-11C>T splice_polypyrimidine_tract_variant, intron_variant NP_653321.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
JAKMIP1ENST00000409021.9 linkuse as main transcriptc.1645-11C>T splice_polypyrimidine_tract_variant, intron_variant 1 NM_001099433.2 ENSP00000386711 P1Q96N16-2

Frequencies

GnomAD3 genomes
AF:
0.0215
AC:
3272
AN:
152176
Hom.:
117
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0736
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00798
Gnomad ASJ
AF:
0.000288
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00949
Gnomad NFE
AF:
0.000808
Gnomad OTH
AF:
0.0205
GnomAD3 exomes
AF:
0.00598
AC:
1501
AN:
250798
Hom.:
47
AF XY:
0.00436
AC XY:
591
AN XY:
135620
show subpopulations
Gnomad AFR exome
AF:
0.0735
Gnomad AMR exome
AF:
0.00500
Gnomad ASJ exome
AF:
0.000595
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000196
Gnomad FIN exome
AF:
0.000143
Gnomad NFE exome
AF:
0.000782
Gnomad OTH exome
AF:
0.00489
GnomAD4 exome
AF:
0.00264
AC:
3806
AN:
1440122
Hom.:
90
Cov.:
27
AF XY:
0.00238
AC XY:
1708
AN XY:
717944
show subpopulations
Gnomad4 AFR exome
AF:
0.0737
Gnomad4 AMR exome
AF:
0.00539
Gnomad4 ASJ exome
AF:
0.000692
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000221
Gnomad4 FIN exome
AF:
0.0000572
Gnomad4 NFE exome
AF:
0.000639
Gnomad4 OTH exome
AF:
0.00610
GnomAD4 genome
AF:
0.0215
AC:
3279
AN:
152294
Hom.:
116
Cov.:
33
AF XY:
0.0202
AC XY:
1501
AN XY:
74476
show subpopulations
Gnomad4 AFR
AF:
0.0735
Gnomad4 AMR
AF:
0.00797
Gnomad4 ASJ
AF:
0.000288
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000809
Gnomad4 OTH
AF:
0.0203
Alfa
AF:
0.00571
Hom.:
31
Bravo
AF:
0.0243
Asia WGS
AF:
0.00520
AC:
18
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.72
CADD
Benign
16
DANN
Benign
0.60

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
0.000016
dbscSNV1_RF
Benign
0.0
SpliceAI score (max)
0.070
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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs16838131; hg19: chr4-6058497; API