chr1-26432282-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The ENST00000434391.6(DHDDS):c.-150G>A variant causes a 5 prime UTR, NMD transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 152,676 control chromosomes in the GnomAD database, including 8,622 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.31 ( 8592 hom., cov: 32)
Exomes 𝑓: 0.26 ( 30 hom. )
Consequence
DHDDS
ENST00000434391.6 5_prime_UTR, NMD_transcript
ENST00000434391.6 5_prime_UTR, NMD_transcript
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.217
Genes affected
DHDDS (HGNC:20603): (dehydrodolichyl diphosphate synthase subunit) The protein encoded by this gene catalyzes cis-prenyl chain elongation to produce the polyprenyl backbone of dolichol, a glycosyl carrier lipid required for the biosynthesis of several classes of glycoproteins. Mutations in this gene are associated with retinitis pigmentosa type 59. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Aug 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=-0.75).
BP6
?
Variant 1-26432282-G-A is Benign according to our data. Variant chr1-26432282-G-A is described in ClinVar as [Benign]. Clinvar id is 297068.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DHDDS | NM_205861.3 | upstream_gene_variant | ENST00000236342.12 | ||||
LOC124903883 | XR_007065557.1 | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DHDDS | ENST00000236342.12 | upstream_gene_variant | 1 | NM_205861.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.309 AC: 47001AN: 152020Hom.: 8589 Cov.: 32
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GnomAD4 exome AF: 0.257 AC: 138AN: 538Hom.: 30 Cov.: 0 AF XY: 0.285 AC XY: 97AN XY: 340
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GnomAD4 genome ? AF: 0.309 AC: 47028AN: 152138Hom.: 8592 Cov.: 32 AF XY: 0.314 AC XY: 23328AN XY: 74388
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Retinitis pigmentosa Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Computational scores
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Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at