rs2230722
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1
The NM_001322198.2(JAK2):c.-632C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 1,611,558 control chromosomes in the GnomAD database, including 79,438 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001322198.2 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
JAK2 | ENST00000381652.4 | c.489C>T | p.His163His | synonymous_variant | Exon 6 of 25 | 1 | NM_004972.4 | ENSP00000371067.4 | ||
JAK2 | ENST00000636127.1 | c.489C>T | p.His163His | synonymous_variant | Exon 6 of 16 | 5 | ENSP00000489812.1 |
Frequencies
GnomAD3 genomes AF: 0.353 AC: 53534AN: 151754Hom.: 9837 Cov.: 32
GnomAD3 exomes AF: 0.322 AC: 80745AN: 250726Hom.: 13270 AF XY: 0.321 AC XY: 43448AN XY: 135536
GnomAD4 exome AF: 0.306 AC: 446694AN: 1459684Hom.: 69592 Cov.: 33 AF XY: 0.306 AC XY: 222429AN XY: 726226
GnomAD4 genome AF: 0.353 AC: 53580AN: 151874Hom.: 9846 Cov.: 32 AF XY: 0.354 AC XY: 26240AN XY: 74212
ClinVar
Submissions by phenotype
not provided Benign:4
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not specified Benign:2
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -
This variant is classified as Benign based on local population frequency. This variant was detected in 48% of patients studied by a panel of primary immunodeficiencies. Number of patients: 42. Only high quality variants are reported. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at