rs62637626
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_004972.4(JAK2):c.3288T>A(p.Asp1096Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000669 in 1,594,448 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_004972.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
JAK2 | NM_004972.4 | c.3288T>A | p.Asp1096Glu | missense_variant | 24/25 | ENST00000381652.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
JAK2 | ENST00000381652.4 | c.3288T>A | p.Asp1096Glu | missense_variant | 24/25 | 1 | NM_004972.4 | P1 | |
INSL6 | ENST00000649639.1 | c.*11-1932A>T | intron_variant | ||||||
JAK2 | ENST00000487310.1 | n.479T>A | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00346 AC: 524AN: 151654Hom.: 4 Cov.: 32
GnomAD3 exomes AF: 0.000954 AC: 232AN: 243216Hom.: 1 AF XY: 0.000692 AC XY: 91AN XY: 131464
GnomAD4 exome AF: 0.000375 AC: 541AN: 1442676Hom.: 5 Cov.: 26 AF XY: 0.000335 AC XY: 241AN XY: 718348
GnomAD4 genome ? AF: 0.00347 AC: 526AN: 151772Hom.: 4 Cov.: 32 AF XY: 0.00323 AC XY: 240AN XY: 74226
ClinVar
Submissions by phenotype
not specified Benign:1Other:1
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Oct 19, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at