15-45116216-C-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_207581.4(DUOXA2):āc.298C>Gā(p.Arg100Gly) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.977 in 1,613,990 control chromosomes in the GnomAD database, including 777,520 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_207581.4 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DUOXA2 | NM_207581.4 | c.298C>G | p.Arg100Gly | missense_variant | 3/6 | ENST00000323030.6 | NP_997464.2 | |
DUOXA2 | XM_017022180.2 | c.298C>G | p.Arg100Gly | missense_variant | 3/6 | XP_016877669.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DUOXA2 | ENST00000323030.6 | c.298C>G | p.Arg100Gly | missense_variant | 3/6 | 1 | NM_207581.4 | ENSP00000319705.5 | ||
DUOXA2 | ENST00000491993.2 | n.*365C>G | non_coding_transcript_exon_variant | 3/6 | 1 | ENSP00000454110.1 | ||||
DUOXA2 | ENST00000491993.2 | n.*365C>G | 3_prime_UTR_variant | 3/6 | 1 | ENSP00000454110.1 | ||||
DUOXA2 | ENST00000350243.10 | n.578C>G | non_coding_transcript_exon_variant | 3/5 | 2 |
Frequencies
GnomAD3 genomes AF: 0.874 AC: 132879AN: 152034Hom.: 61037 Cov.: 32
GnomAD3 exomes AF: 0.969 AC: 241874AN: 249510Hom.: 118692 AF XY: 0.977 AC XY: 132260AN XY: 135382
GnomAD4 exome AF: 0.988 AC: 1443770AN: 1461838Hom.: 716472 Cov.: 73 AF XY: 0.989 AC XY: 719544AN XY: 727210
GnomAD4 genome AF: 0.874 AC: 132937AN: 152152Hom.: 61048 Cov.: 32 AF XY: 0.880 AC XY: 65467AN XY: 74390
ClinVar
Submissions by phenotype
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 | - | - - |
Thyroglobulin synthesis defect Benign:2
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Benign, criteria provided, single submitter | clinical testing | Mendelics | May 28, 2019 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 05, 2018 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at