17-82037555-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_016286.4(DCXR):​c.53-8C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00481 in 1,544,190 control chromosomes in the GnomAD database, including 348 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.026 ( 198 hom., cov: 34)
Exomes 𝑓: 0.0025 ( 150 hom. )

Consequence

DCXR
NM_016286.4 splice_region, intron

Scores

2
Splicing: ADA: 0.0002313
2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.0440
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
Variant 17-82037555-G-A is Benign according to our data. Variant chr17-82037555-G-A is described in ClinVar as [Benign]. Clinvar id is 711695.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0883 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
DCXRNM_016286.4 linkc.53-8C>T splice_region_variant, intron_variant Intron 1 of 7 ENST00000306869.7 NP_057370.1 Q7Z4W1A0A384NY14
DCXRNM_001195218.1 linkc.53-14C>T intron_variant Intron 1 of 7 NP_001182147.1 Q7Z4W1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
DCXRENST00000306869.7 linkc.53-8C>T splice_region_variant, intron_variant Intron 1 of 7 1 NM_016286.4 ENSP00000303356.2 Q7Z4W1

Frequencies

GnomAD3 genomes
AF:
0.0257
AC:
3908
AN:
152216
Hom.:
198
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.0908
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00635
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00637
Gnomad NFE
AF:
0.000147
Gnomad OTH
AF:
0.0167
GnomAD3 exomes
AF:
0.00531
AC:
750
AN:
141280
Hom.:
35
AF XY:
0.00396
AC XY:
308
AN XY:
77874
show subpopulations
Gnomad AFR exome
AF:
0.0934
Gnomad AMR exome
AF:
0.00342
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000172
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000128
Gnomad OTH exome
AF:
0.00312
GnomAD4 exome
AF:
0.00252
AC:
3509
AN:
1391860
Hom.:
150
Cov.:
32
AF XY:
0.00218
AC XY:
1498
AN XY:
687948
show subpopulations
Gnomad4 AFR exome
AF:
0.0941
Gnomad4 AMR exome
AF:
0.00387
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000250
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000388
Gnomad4 OTH exome
AF:
0.00539
GnomAD4 genome
AF:
0.0257
AC:
3915
AN:
152330
Hom.:
198
Cov.:
34
AF XY:
0.0245
AC XY:
1828
AN XY:
74494
show subpopulations
Gnomad4 AFR
AF:
0.0907
Gnomad4 AMR
AF:
0.00634
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000147
Gnomad4 OTH
AF:
0.0165
Alfa
AF:
0.0115
Hom.:
11
Bravo
AF:
0.0285
Asia WGS
AF:
0.00346
AC:
12
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
-
Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided

- -

Jun 14, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
7.8
DANN
Benign
0.95

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
0.00023
dbscSNV1_RF
Benign
0.034
SpliceAI score (max)
0.040
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: rs12946979; hg19: chr17-79995431; API