rs269868
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001363711.2(DUOX2):c.3200C>T(p.Ser1067Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.889 in 1,613,952 control chromosomes in the GnomAD database, including 655,306 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin ClinVar.
Frequency
Consequence
NM_001363711.2 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 |
---|---|---|---|---|---|---|---|
DUOX2 | NM_001363711.2 | c.3200C>T | p.Ser1067Leu | missense_variant | 25/34 | ENST00000389039.11 | |
DUOX2 | NM_014080.5 | c.3200C>T | p.Ser1067Leu | missense_variant | 25/34 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DUOX2 | ENST00000389039.11 | c.3200C>T | p.Ser1067Leu | missense_variant | 25/34 | 1 | NM_001363711.2 | P4 | |
DUOX2 | ENST00000603300.1 | c.3200C>T | p.Ser1067Leu | missense_variant | 25/34 | 1 | A1 | ||
DUOX2 | ENST00000558383.1 | n.5972C>T | non_coding_transcript_exon_variant | 16/17 | 5 | ||||
DUOX2 | ENST00000560797.1 | n.380C>T | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.734 AC: 111516AN: 151994Hom.: 47671 Cov.: 32
GnomAD3 exomes AF: 0.875 AC: 219774AN: 251092Hom.: 99867 AF XY: 0.890 AC XY: 120799AN XY: 135798
GnomAD4 exome AF: 0.905 AC: 1323562AN: 1461838Hom.: 607648 Cov.: 63 AF XY: 0.909 AC XY: 660817AN XY: 727224
GnomAD4 genome ? AF: 0.733 AC: 111506AN: 152114Hom.: 47658 Cov.: 32 AF XY: 0.742 AC XY: 55203AN XY: 74352
ClinVar
Submissions by phenotype
Thyroid dyshormonogenesis 6 Benign:4
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Benign, criteria provided, single submitter | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | Sep 21, 2015 | - - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Mar 06, 2018 | 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. - |
Benign, criteria provided, single submitter | clinical testing | Mendelics | May 28, 2019 | - - |
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at