14-24291558-G-A

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001136050.3(DHRS1):​c.722C>T​(p.Thr241Ile) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.0683 in 1,613,984 control chromosomes in the GnomAD database, including 4,223 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.

Frequency

Genomes: 𝑓 0.085 ( 611 hom., cov: 32)
Exomes 𝑓: 0.067 ( 3612 hom. )

Consequence

DHRS1
NM_001136050.3 missense, splice_region

Scores

1
6
10
Splicing: ADA: 0.9999
2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.80
Variant links:
Genes affected
DHRS1 (HGNC:16445): (dehydrogenase/reductase 1) This gene encodes a member of the short-chain dehydrogenases/reductases (SDR) family. The encoded enzyme contains a conserved catalytic domain and likely functions as an oxidoreductase. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Nov 2008]
NOP9 (HGNC:19826): (NOP9 nucleolar protein) Enables RNA binding activity. Predicted to be involved in ribosome biogenesis. Predicted to be part of 90S preribosome and preribosome, small subunit precursor. Predicted to be active in nucleolus. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
DHRS1NM_001136050.3 linkc.722C>T p.Thr241Ile missense_variant, splice_region_variant Exon 7 of 9 ENST00000288111.12 NP_001129522.1 Q96LJ7

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
DHRS1ENST00000288111.12 linkc.722C>T p.Thr241Ile missense_variant, splice_region_variant Exon 7 of 9 1 NM_001136050.3 ENSP00000288111.7 Q96LJ7

Frequencies

GnomAD3 genomes
AF:
0.0853
AC:
12982
AN:
152116
Hom.:
611
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.130
Gnomad AMI
AF:
0.114
Gnomad AMR
AF:
0.0652
Gnomad ASJ
AF:
0.102
Gnomad EAS
AF:
0.0746
Gnomad SAS
AF:
0.0953
Gnomad FIN
AF:
0.0535
Gnomad MID
AF:
0.0728
Gnomad NFE
AF:
0.0670
Gnomad OTH
AF:
0.0756
GnomAD3 exomes
AF:
0.0754
AC:
18951
AN:
251492
Hom.:
818
AF XY:
0.0768
AC XY:
10436
AN XY:
135920
show subpopulations
Gnomad AFR exome
AF:
0.131
Gnomad AMR exome
AF:
0.0623
Gnomad ASJ exome
AF:
0.109
Gnomad EAS exome
AF:
0.0838
Gnomad SAS exome
AF:
0.100
Gnomad FIN exome
AF:
0.0516
Gnomad NFE exome
AF:
0.0649
Gnomad OTH exome
AF:
0.0752
GnomAD4 exome
AF:
0.0665
AC:
97237
AN:
1461750
Hom.:
3612
Cov.:
31
AF XY:
0.0682
AC XY:
49594
AN XY:
727190
show subpopulations
Gnomad4 AFR exome
AF:
0.130
Gnomad4 AMR exome
AF:
0.0647
Gnomad4 ASJ exome
AF:
0.110
Gnomad4 EAS exome
AF:
0.0605
Gnomad4 SAS exome
AF:
0.100
Gnomad4 FIN exome
AF:
0.0510
Gnomad4 NFE exome
AF:
0.0616
Gnomad4 OTH exome
AF:
0.0709
GnomAD4 genome
AF:
0.0853
AC:
12988
AN:
152234
Hom.:
611
Cov.:
32
AF XY:
0.0850
AC XY:
6331
AN XY:
74458
show subpopulations
Gnomad4 AFR
AF:
0.130
Gnomad4 AMR
AF:
0.0653
Gnomad4 ASJ
AF:
0.102
Gnomad4 EAS
AF:
0.0744
Gnomad4 SAS
AF:
0.0956
Gnomad4 FIN
AF:
0.0535
Gnomad4 NFE
AF:
0.0670
Gnomad4 OTH
AF:
0.0748
Alfa
AF:
0.0732
Hom.:
1056
Bravo
AF:
0.0866
TwinsUK
AF:
0.0529
AC:
196
ALSPAC
AF:
0.0599
AC:
231
ESP6500AA
AF:
0.124
AC:
545
ESP6500EA
AF:
0.0700
AC:
602
ExAC
AF:
0.0759
AC:
9209
Asia WGS
AF:
0.0750
AC:
259
AN:
3478
EpiCase
AF:
0.0707
EpiControl
AF:
0.0670

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.23
BayesDel_addAF
Benign
-0.35
T
BayesDel_noAF
Benign
-0.16
CADD
Uncertain
26
DANN
Uncertain
1.0
DEOGEN2
Benign
0.023
T;T
Eigen
Uncertain
0.32
Eigen_PC
Uncertain
0.44
FATHMM_MKL
Uncertain
0.93
D
MetaRNN
Benign
0.0026
T;T
MetaSVM
Benign
-0.62
T
MutationAssessor
Pathogenic
3.0
M;M
PrimateAI
Uncertain
0.61
T
PROVEAN
Benign
-2.1
N;N
REVEL
Uncertain
0.38
Sift
Benign
0.065
T;T
Sift4G
Benign
0.16
T;T
Polyphen
0.34
B;B
Vest4
0.12
MPC
0.19
ClinPred
0.033
T
GERP RS
6.0
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.17
gMVP
0.56

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Pathogenic
1.0
dbscSNV1_RF
Pathogenic
0.99
SpliceAI score (max)
0.20
Details are displayed if max score is > 0.2
DS_DL_spliceai
0.20
Position offset: -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: rs10134537; hg19: chr14-24760764; COSMIC: COSV55384222; COSMIC: COSV55384222; API