14-23638942-C-A
Variant names:
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_005794.4(DHRS2):c.78C>A(p.Thr26Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000657 in 1,614,104 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0037 ( 3 hom., cov: 32)
Exomes 𝑓: 0.00034 ( 2 hom. )
Consequence
DHRS2
NM_005794.4 synonymous
NM_005794.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.350
Genes affected
DHRS2 (HGNC:18349): (dehydrogenase/reductase 2) This gene encodes a member of the short-chain dehydrogenases/reductases (SDR) family, which has over 46,000 members. Members of this family are enzymes that metabolize many different compounds, such as steroid hormones, prostaglandins, retinoids, lipids and xenobiotics. Alternative promoter use and alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.6).
BP6
Variant 14-23638942-C-A is Benign according to our data. Variant chr14-23638942-C-A is described in ClinVar as [Benign]. Clinvar id is 782584.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.35 with no splicing effect.
BS2
High Homozygotes in GnomAd4 at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DHRS2 | NM_005794.4 | c.78C>A | p.Thr26Thr | synonymous_variant | Exon 2 of 9 | ENST00000250383.11 | NP_005785.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00358 AC: 545AN: 152180Hom.: 2 Cov.: 32
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GnomAD3 exomes AF: 0.000855 AC: 215AN: 251422Hom.: 2 AF XY: 0.000574 AC XY: 78AN XY: 135880
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GnomAD4 exome AF: 0.000342 AC: 500AN: 1461806Hom.: 2 Cov.: 31 AF XY: 0.000287 AC XY: 209AN XY: 727210
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GnomAD4 genome AF: 0.00368 AC: 560AN: 152298Hom.: 3 Cov.: 32 AF XY: 0.00352 AC XY: 262AN XY: 74478
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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
Aug 24, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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