10-132104867-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001323087.2(JAKMIP3):c.59C>T(p.Ala20Val) variant causes a missense change. The variant allele was found at a frequency of 0.00000896 in 1,563,168 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001323087.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
JAKMIP3 | NM_001323087.2 | c.59C>T | p.Ala20Val | missense_variant | Exon 2 of 24 | ENST00000684848.1 | NP_001310016.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
JAKMIP3 | ENST00000684848.1 | c.59C>T | p.Ala20Val | missense_variant | Exon 2 of 24 | NM_001323087.2 | ENSP00000508932.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152224Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000574 AC: 1AN: 174224Hom.: 0 AF XY: 0.0000108 AC XY: 1AN XY: 92868
GnomAD4 exome AF: 0.00000850 AC: 12AN: 1410944Hom.: 0 Cov.: 30 AF XY: 0.0000115 AC XY: 8AN XY: 697026
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152224Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74366
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.59C>T (p.A20V) alteration is located in exon 1 (coding exon 1) of the JAKMIP3 gene. This alteration results from a C to T substitution at nucleotide position 59, causing the alanine (A) at amino acid position 20 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at