rs2554459
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_207581.4(DUOXA2):c.341-4A>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,613,484 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_207581.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DUOXA2 | NM_207581.4 | c.341-4A>C | splice_region_variant, intron_variant | ENST00000323030.6 | NP_997464.2 | |||
DUOXA2 | XM_017022180.2 | c.388A>C | p.Thr130Pro | missense_variant | 4/6 | XP_016877669.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DUOXA2 | ENST00000323030.6 | c.341-4A>C | splice_region_variant, intron_variant | 1 | NM_207581.4 | ENSP00000319705.5 | ||||
DUOXA2 | ENST00000491993.2 | n.*408-4A>C | splice_region_variant, intron_variant | 1 | ENSP00000454110.1 | |||||
DUOXA2 | ENST00000350243.10 | n.621-4A>C | splice_region_variant, intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152168Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000803 AC: 2AN: 248988Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135212
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461316Hom.: 0 Cov.: 59 AF XY: 0.0000151 AC XY: 11AN XY: 726992
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152168Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74346
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at