chr9-5126321-GGTTT-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.
The NM_004972.4(JAK2):c.3178-7_3178-4del variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000718 in 1,393,384 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004972.4 splice_region, splice_polypyrimidine_tract, intron
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
JAK2 | NM_004972.4 | c.3178-7_3178-4del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000381652.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
JAK2 | ENST00000381652.4 | c.3178-7_3178-4del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_004972.4 | P1 | |||
INSL6 | ENST00000649639.1 | c.*11-1814_*11-1811del | intron_variant | ||||||
JAK2 | ENST00000487310.1 | n.362_365del | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000869 AC: 2AN: 230054Hom.: 0 AF XY: 0.0000161 AC XY: 2AN XY: 124558
GnomAD4 exome AF: 0.00000718 AC: 10AN: 1393384Hom.: 0 AF XY: 0.00000719 AC XY: 5AN XY: 695396
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jan 26, 2023 | This variant has not been reported in the literature in individuals affected with JAK2-related conditions. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. This variant is present in population databases (rs755963730, gnomAD 0.01%). This sequence change falls in intron 23 of the JAK2 gene. It does not directly change the encoded amino acid sequence of the JAK2 protein. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at