GeneBe

rs375747326

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_015954.4(DERA):​c.313C>G​(p.Arg105Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R105W) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

DERA
NM_015954.4 missense

Scores

5
7
6

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 3.08

Publications

3 publications found
Variant links:
Genes affected
DERA (HGNC:24269): (deoxyribose-phosphate aldolase) Enables deoxyribose-phosphate aldolase activity. Involved in deoxyribonucleoside catabolic process. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015954.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
DERA
NM_015954.4
MANE Select
c.313C>Gp.Arg105Gly
missense
Exon 4 of 9NP_057038.2Q9Y315
DERA
NM_001300779.2
c.313C>Gp.Arg105Gly
missense
Exon 4 of 8NP_001287708.1E9PPM8

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
DERA
ENST00000428559.7
TSL:1 MANE Select
c.313C>Gp.Arg105Gly
missense
Exon 4 of 9ENSP00000416583.2Q9Y315
DERA
ENST00000526530.1
TSL:1
c.49C>Gp.Arg17Gly
missense
Exon 4 of 9ENSP00000431757.1G3V158
DERA
ENST00000885123.1
c.313C>Gp.Arg105Gly
missense
Exon 4 of 9ENSP00000555182.1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1398642
Hom.:
0
Cov.:
30
AF XY:
0.00
AC XY:
0
AN XY:
689988
African (AFR)
AF:
0.00
AC:
0
AN:
31726
American (AMR)
AF:
0.00
AC:
0
AN:
36068
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
25226
East Asian (EAS)
AF:
0.00
AC:
0
AN:
36024
South Asian (SAS)
AF:
0.00
AC:
0
AN:
79132
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
49364
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5692
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
1077464
Other (OTH)
AF:
0.00
AC:
0
AN:
57946
GnomAD4 genome
Cov.:
32
Alfa
AF:
0.00
Hom.:
0
Bravo
AF:
0.0000264

ClinVar

ClinVar submissions
Significance:Uncertain significance
Revision:criteria provided, single submitter
View on ClinVar
Pathogenic
VUS
Benign
Condition
-
1
-
not specified (1)

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.53
BayesDel_addAF
Pathogenic
0.39
D
BayesDel_noAF
Pathogenic
0.33
CADD
Uncertain
24
DANN
Benign
0.96
DEOGEN2
Uncertain
0.58
D
Eigen
Benign
0.11
Eigen_PC
Benign
-0.085
FATHMM_MKL
Uncertain
0.91
D
LIST_S2
Pathogenic
0.98
D
M_CAP
Benign
0.080
D
MetaRNN
Uncertain
0.72
D
MetaSVM
Uncertain
-0.27
T
MutationAssessor
Pathogenic
3.2
M
PhyloP100
3.1
PrimateAI
Uncertain
0.68
T
PROVEAN
Pathogenic
-4.6
D
REVEL
Uncertain
0.41
Sift
Benign
0.13
T
Sift4G
Benign
0.35
T
Polyphen
1.0
D
Vest4
0.87
MutPred
0.69
Loss of stability (P = 0.0412)
MVP
0.41
MPC
0.32
ClinPred
0.99
D
GERP RS
3.2
Varity_R
0.83
gMVP
0.90
Mutation Taster
=29/71
disease causing

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

Other links and lift over

dbSNP: rs375747326; hg19: chr12-16112798; API