rs3830585
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_139276.3(STAT3):c.1601-8dupT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 1,613,038 control chromosomes in the GnomAD database, including 53,571 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_139276.3 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.338 AC: 51335AN: 151992Hom.: 12179 Cov.: 0
GnomAD3 exomes AF: 0.246 AC: 61687AN: 250758Hom.: 9911 AF XY: 0.244 AC XY: 33060AN XY: 135576
GnomAD4 exome AF: 0.220 AC: 320944AN: 1460928Hom.: 41351 Cov.: 32 AF XY: 0.222 AC XY: 161210AN XY: 726838
GnomAD4 genome AF: 0.338 AC: 51437AN: 152110Hom.: 12220 Cov.: 0 AF XY: 0.338 AC XY: 25095AN XY: 74352
ClinVar
Submissions by phenotype
not specified Benign:3
Benign based on high population prevalence -
This variant is classified as Benign based on local population frequency. This variant was detected in 35% of patients studied by a panel of primary immunodeficiencies. Number of patients: 34. Only high quality variants are reported. -
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not provided Benign:1Other:1
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Variant interpreted as Benign and reported on 04-27-2020 by Lab or GTR ID 500031. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. This variant was reported in an individual referred for clinical diagnostic genetic testing. -
STAT3-related early-onset multisystem autoimmune disease Benign:1
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Hyper-IgE recurrent infection syndrome 1, autosomal dominant Benign:1
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Hyper-IgE syndrome Benign:1
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Hyper-IgE recurrent infection syndrome 1, autosomal dominant;C4288261:STAT3 gain of function Benign:1
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Hyper-IgE recurrent infection syndrome 1, autosomal dominant;C4014795:STAT3-related early-onset multisystem autoimmune disease Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at