rs1006771
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001084393.2(DDTL):c.*411G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.658 in 600,156 control chromosomes in the GnomAD database, including 130,583 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 0.67 ( 33832 hom., cov: 32)
Exomes 𝑓: 0.65 ( 96751 hom. )
Consequence
DDTL
NM_001084393.2 3_prime_UTR
NM_001084393.2 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.53
Genes affected
DDTL (HGNC:33446): (D-dopachrome tautomerase like) Predicted to enable lyase activity. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]
DDT (HGNC:2732): (D-dopachrome tautomerase) D-dopachrome tautomerase converts D-dopachrome into 5,6-dihydroxyindole. The DDT gene is related to the migration inhibitory factor (MIF) in terms of sequence, enzyme activity, and gene structure. DDT and MIF are closely linked on chromosome 22. [provided by RefSeq, Jul 2008]
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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=-0.84).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.714 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DDTL | NM_001084393.2 | c.*411G>T | 3_prime_UTR_variant | 3/3 | ENST00000215770.6 | ||
DDT | NM_001084392.3 | c.285-194C>A | intron_variant | ENST00000398344.9 | |||
DDT | NM_001355.4 | c.285-194C>A | intron_variant | ||||
DDT | NM_001397485.1 | c.285-194C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DDTL | ENST00000215770.6 | c.*411G>T | 3_prime_UTR_variant | 3/3 | 2 | NM_001084393.2 | P1 | ||
DDT | ENST00000398344.9 | c.285-194C>A | intron_variant | 1 | NM_001084392.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.668 AC: 101132AN: 151378Hom.: 33811 Cov.: 32
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GnomAD4 exome AF: 0.654 AC: 293462AN: 448662Hom.: 96751 Cov.: 4 AF XY: 0.657 AC XY: 155192AN XY: 236090
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GnomAD4 genome ? AF: 0.668 AC: 101203AN: 151494Hom.: 33832 Cov.: 32 AF XY: 0.673 AC XY: 49777AN XY: 73972
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at