rs9584234
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000377028.10(DCT):c.1179+686G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 152,162 control chromosomes in the GnomAD database, including 1,643 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.14 ( 1643 hom., cov: 32)
Consequence
DCT
ENST00000377028.10 intron
ENST00000377028.10 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.459
Genes affected
DCT (HGNC:2709): (dopachrome tautomerase) Predicted to enable dopachrome isomerase activity. Involved in response to blue light. Located in intracellular membrane-bounded organelle and plasma membrane. Implicated in oculocutaneous albinism. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.186 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DCT | NM_001922.5 | c.1179+686G>A | intron_variant | ENST00000377028.10 | NP_001913.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DCT | ENST00000377028.10 | c.1179+686G>A | intron_variant | 1 | NM_001922.5 | ENSP00000366227 | P1 | |||
DCT | ENST00000446125.1 | c.1179+686G>A | intron_variant | 1 | ENSP00000392762 | |||||
DCT | ENST00000483392.6 | c.609+686G>A | intron_variant, NMD_transcript_variant | 5 | ENSP00000431275 |
Frequencies
GnomAD3 genomes AF: 0.142 AC: 21571AN: 152044Hom.: 1642 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.142 AC: 21602AN: 152162Hom.: 1643 Cov.: 32 AF XY: 0.142 AC XY: 10553AN XY: 74390
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605
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ClinVar
Not reported inComputational scores
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Name
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at