GeneBe

NM_001367834.3:c.92G>A

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001367834.3(ZSWIM4):​c.92G>A​(p.Arg31Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R31G) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 31)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

ZSWIM4
NM_001367834.3 missense

Scores

1
2
15

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.15

Publications

0 publications found
Variant links:
Genes affected
ZSWIM4 (HGNC:25704): (zinc finger SWIM-type containing 4) Predicted to enable zinc ion binding activity. Predicted to be part of Cul2-RING ubiquitin ligase complex. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.11470476).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001367834.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
ZSWIM4
NM_001367834.3
MANE Select
c.92G>Ap.Arg31Gln
missense
Exon 1 of 14NP_001354763.1K7ERJ6
ZSWIM4
NM_023072.3
c.92G>Ap.Arg31Gln
missense
Exon 1 of 13NP_075560.2Q9H7M6

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
ZSWIM4
ENST00000590508.6
TSL:2 MANE Select
c.92G>Ap.Arg31Gln
missense
Exon 1 of 14ENSP00000468285.2K7ERJ6
ZSWIM4
ENST00000938264.1
c.92G>Ap.Arg31Gln
missense
Exon 1 of 15ENSP00000608323.1
ZSWIM4
ENST00000938266.1
c.92G>Ap.Arg31Gln
missense
Exon 1 of 14ENSP00000608325.1

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1073356
Hom.:
0
Cov.:
30
AF XY:
0.00
AC XY:
0
AN XY:
507388
African (AFR)
AF:
0.00
AC:
0
AN:
22882
American (AMR)
AF:
0.00
AC:
0
AN:
8398
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
13800
East Asian (EAS)
AF:
0.00
AC:
0
AN:
26404
South Asian (SAS)
AF:
0.00
AC:
0
AN:
19996
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
20946
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
2962
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
915036
Other (OTH)
AF:
0.00
AC:
0
AN:
42932
GnomAD4 genome
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.11
BayesDel_addAF
Benign
-0.13
T
BayesDel_noAF
Benign
-0.43
CADD
Benign
21
DANN
Uncertain
0.99
DEOGEN2
Benign
0.0095
T
Eigen
Benign
-0.49
Eigen_PC
Benign
-0.43
FATHMM_MKL
Benign
0.40
N
LIST_S2
Benign
0.63
T
M_CAP
Uncertain
0.23
D
MetaRNN
Benign
0.11
T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
0.46
N
PhyloP100
1.2
PrimateAI
Pathogenic
0.88
D
PROVEAN
Benign
-0.070
N
REVEL
Benign
0.032
Sift
Benign
0.62
T
Sift4G
Benign
0.50
T
Polyphen
0.26
B
Vest4
0.10
MutPred
0.23
Loss of methylation at R31 (P = 0.0055)
MVP
0.31
MPC
0.69
ClinPred
0.60
D
GERP RS
3.7
PromoterAI
-0.030
Neutral
Varity_R
0.11
gMVP
0.14
Mutation Taster
=91/9
polymorphism

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

Other links and lift over

dbSNP: rs1484828467; hg19: chr19-13906554; API