17-82036724-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_016286.4(DCXR):​c.345G>A​(p.Ser115Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 1,613,272 control chromosomes in the GnomAD database, including 23,273 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.24 ( 7672 hom., cov: 33)
Exomes 𝑓: 0.12 ( 15601 hom. )

Consequence

DCXR
NM_016286.4 synonymous

Scores

2

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.541
Variant links:
Genes affected
DCXR (HGNC:18985): (dicarbonyl and L-xylulose reductase) The protein encoded by this gene acts as a homotetramer to catalyze diacetyl reductase and L-xylulose reductase reactions. The encoded protein may play a role in the uronate cycle of glucose metabolism and in the cellular osmoregulation in the proximal renal tubules. Defects in this gene are a cause of pentosuria. Two transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Aug 2010]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.72).
BP6
Variant 17-82036724-C-T is Benign according to our data. Variant chr17-82036724-C-T is described in ClinVar as [Benign]. Clinvar id is 3055361.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
Synonymous conserved (PhyloP=-0.541 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
DCXRNM_016286.4 linkc.345G>A p.Ser115Ser synonymous_variant Exon 4 of 8 ENST00000306869.7 NP_057370.1 Q7Z4W1A0A384NY14
DCXRNM_001195218.1 linkc.339G>A p.Ser113Ser synonymous_variant Exon 4 of 8 NP_001182147.1 Q7Z4W1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
DCXRENST00000306869.7 linkc.345G>A p.Ser115Ser synonymous_variant Exon 4 of 8 1 NM_016286.4 ENSP00000303356.2 Q7Z4W1

Frequencies

GnomAD3 genomes
AF:
0.240
AC:
36521
AN:
151862
Hom.:
7633
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.573
Gnomad AMI
AF:
0.0987
Gnomad AMR
AF:
0.120
Gnomad ASJ
AF:
0.0470
Gnomad EAS
AF:
0.0674
Gnomad SAS
AF:
0.0253
Gnomad FIN
AF:
0.149
Gnomad MID
AF:
0.0886
Gnomad NFE
AF:
0.123
Gnomad OTH
AF:
0.185
GnomAD3 exomes
AF:
0.128
AC:
32069
AN:
250784
Hom.:
4148
AF XY:
0.117
AC XY:
15823
AN XY:
135772
show subpopulations
Gnomad AFR exome
AF:
0.584
Gnomad AMR exome
AF:
0.0664
Gnomad ASJ exome
AF:
0.0510
Gnomad EAS exome
AF:
0.0697
Gnomad SAS exome
AF:
0.0229
Gnomad FIN exome
AF:
0.152
Gnomad NFE exome
AF:
0.123
Gnomad OTH exome
AF:
0.105
GnomAD4 exome
AF:
0.123
AC:
179249
AN:
1461292
Hom.:
15601
Cov.:
34
AF XY:
0.118
AC XY:
85747
AN XY:
726930
show subpopulations
Gnomad4 AFR exome
AF:
0.587
Gnomad4 AMR exome
AF:
0.0718
Gnomad4 ASJ exome
AF:
0.0503
Gnomad4 EAS exome
AF:
0.0646
Gnomad4 SAS exome
AF:
0.0241
Gnomad4 FIN exome
AF:
0.152
Gnomad4 NFE exome
AF:
0.121
Gnomad4 OTH exome
AF:
0.124
GnomAD4 genome
AF:
0.241
AC:
36615
AN:
151980
Hom.:
7672
Cov.:
33
AF XY:
0.235
AC XY:
17488
AN XY:
74316
show subpopulations
Gnomad4 AFR
AF:
0.574
Gnomad4 AMR
AF:
0.119
Gnomad4 ASJ
AF:
0.0470
Gnomad4 EAS
AF:
0.0676
Gnomad4 SAS
AF:
0.0249
Gnomad4 FIN
AF:
0.149
Gnomad4 NFE
AF:
0.123
Gnomad4 OTH
AF:
0.183
Alfa
AF:
0.167
Hom.:
1918
Bravo
AF:
0.253
Asia WGS
AF:
0.0830
AC:
289
AN:
3478
EpiCase
AF:
0.104
EpiControl
AF:
0.103

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

DCXR-related disorder Benign:1
Oct 28, 2019
PreventionGenetics, part of Exact Sciences
Significance: Benign
Review Status: no assertion criteria provided
Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.72
CADD
Benign
3.7
DANN
Benign
0.91
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs9780; hg19: chr17-79994600; COSMIC: COSV60956272; COSMIC: COSV60956272; API