NM_002227.4:c.*3A>C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_002227.4(JAK1):c.*3A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000763 in 1,573,682 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_002227.4 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152250Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 247898Hom.: 0 AF XY: 0.0000223 AC XY: 3AN XY: 134448
GnomAD4 exome AF: 0.00000422 AC: 6AN: 1421314Hom.: 0 Cov.: 25 AF XY: 0.00000423 AC XY: 3AN XY: 709430
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152368Hom.: 0 Cov.: 33 AF XY: 0.0000671 AC XY: 5AN XY: 74516
ClinVar
Submissions by phenotype
JAK1-related disorder Uncertain:1
The JAK1 c.*3A>C variant is located in the 3' untranslated region. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.017% of alleles in individuals of African descent in gnomAD (http://gnomad.broadinstitute.org/variant/1-65300242-T-G). Although we suspect that this variant may be benign, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at