rs11575543
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001082971.2(DDC):c.*18+42C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0217 in 1,511,196 control chromosomes in the GnomAD database, including 1,012 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.051 ( 437 hom., cov: 32)
Exomes 𝑓: 0.018 ( 575 hom. )
Consequence
DDC
NM_001082971.2 intron
NM_001082971.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.10
Genes affected
DDC (HGNC:2719): (dopa decarboxylase) The encoded protein catalyzes the decarboxylation of L-3,4-dihydroxyphenylalanine (DOPA) to dopamine, L-5-hydroxytryptophan to serotonin and L-tryptophan to tryptamine. Defects in this gene are the cause of aromatic L-amino-acid decarboxylase deficiency (AADCD). AADCD deficiency is an inborn error in neurotransmitter metabolism that leads to combined serotonin and catecholamine deficiency. Multiple alternatively spliced transcript variants encoding different isoforms have been identified for this gene. [provided by RefSeq, Jun 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
?
Variant 7-50463171-G-A is Benign according to our data. Variant chr7-50463171-G-A is described in ClinVar as [Benign]. Clinvar id is 1222837.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DDC | NM_001082971.2 | c.*18+42C>T | intron_variant | ENST00000444124.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DDC | ENST00000444124.7 | c.*18+42C>T | intron_variant | 1 | NM_001082971.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0505 AC: 7678AN: 152134Hom.: 433 Cov.: 32
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GnomAD4 exome AF: 0.0184 AC: 25051AN: 1358944Hom.: 575 Cov.: 24 AF XY: 0.0179 AC XY: 12036AN XY: 673112
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GnomAD4 genome ? AF: 0.0507 AC: 7712AN: 152252Hom.: 437 Cov.: 32 AF XY: 0.0487 AC XY: 3627AN XY: 74450
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 12, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
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Dann
Benign
RBP_binding_hub_radar
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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