rs16838131
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
Consequence
NM_001099433.2 splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
JAKMIP1 | NM_001099433.2 | c.1645-11C>T | splice_polypyrimidine_tract_variant, intron_variant | ENST00000409021.9 | NP_001092903.1 | |||
JAKMIP1 | NM_001306133.2 | c.1645-11C>T | splice_polypyrimidine_tract_variant, intron_variant | NP_001293062.1 | ||||
JAKMIP1 | NM_001306134.2 | c.1150-11C>T | splice_polypyrimidine_tract_variant, intron_variant | NP_001293063.1 | ||||
JAKMIP1 | NM_144720.4 | c.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 |
---|---|---|---|---|---|---|---|---|---|---|
JAKMIP1 | ENST00000409021.9 | c.1645-11C>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001099433.2 | ENSP00000386711 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0215 AC: 3272AN: 152176Hom.: 117 Cov.: 33
GnomAD3 exomes AF: 0.00598 AC: 1501AN: 250798Hom.: 47 AF XY: 0.00436 AC XY: 591AN XY: 135620
GnomAD4 exome AF: 0.00264 AC: 3806AN: 1440122Hom.: 90 Cov.: 27 AF XY: 0.00238 AC XY: 1708AN XY: 717944
GnomAD4 genome AF: 0.0215 AC: 3279AN: 152294Hom.: 116 Cov.: 33 AF XY: 0.0202 AC XY: 1501AN XY: 74476
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at