rs118101939
Variant summary
Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_000215.4(JAK3):c.*1319G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0133 in 218,150 control chromosomes in the GnomAD database, including 35 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_000215.4 3_prime_UTR
Scores
Clinical Significance
Conservation
Publications
- T-B+ severe combined immunodeficiency due to JAK3 deficiencyInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, Labcorp Genetics (formerly Invitae), Laboratory for Molecular Medicine, ClinGen, Orphanet
Genome browser will be placed here
ACMG classification
Our verdict: Benign. The variant received -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
JAK3 | NM_000215.4 | c.*1319G>A | 3_prime_UTR_variant | Exon 24 of 24 | ENST00000458235.7 | NP_000206.2 | ||
JAK3 | NM_001440439.1 | c.*1319G>A | 3_prime_UTR_variant | Exon 24 of 24 | NP_001427368.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
JAK3 | ENST00000458235.7 | c.*1319G>A | 3_prime_UTR_variant | Exon 24 of 24 | 5 | NM_000215.4 | ENSP00000391676.1 | |||
JAK3 | ENST00000696967.1 | n.3871G>A | non_coding_transcript_exon_variant | Exon 19 of 19 | ||||||
JAK3 | ENST00000696968.1 | n.1927G>A | non_coding_transcript_exon_variant | Exon 3 of 3 | ||||||
JAK3 | ENST00000527031.5 | n.2279-114G>A | intron_variant | Intron 13 of 13 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0138 AC: 2098AN: 152042Hom.: 29 Cov.: 32 show subpopulations
GnomAD4 exome AF: 0.0123 AC: 814AN: 65990Hom.: 6 Cov.: 0 AF XY: 0.0125 AC XY: 384AN XY: 30620 show subpopulations
GnomAD4 genome AF: 0.0138 AC: 2098AN: 152160Hom.: 29 Cov.: 32 AF XY: 0.0129 AC XY: 959AN XY: 74386 show subpopulations
ClinVar
Submissions by phenotype
T-B+ severe combined immunodeficiency due to JAK3 deficiency Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at