GeneBe

rs1984078380

Variant names:

Variant summary

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

The NM_033129.4(SCRT2):​c.281G>T​(p.Arg94Leu) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

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

Consequence

SCRT2
NM_033129.4 missense

Scores

2
2
14

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.80

Publications

0 publications found
Variant links:
Genes affected
SCRT2 (HGNC:15952): (scratch family transcriptional repressor 2) Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in negative regulation of extrinsic apoptotic signaling pathway via death domain receptors and negative regulation of transcription by RNA polymerase II. Predicted to act upstream of or within regulation of neuron migration. Predicted to be located in chromatin. [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 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.20989648).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_033129.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
SCRT2
NM_033129.4
MANE Select
c.281G>Tp.Arg94Leu
missense
Exon 2 of 2NP_149120.1Q9NQ03

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
SCRT2
ENST00000246104.7
TSL:1 MANE Select
c.281G>Tp.Arg94Leu
missense
Exon 2 of 2ENSP00000246104.5Q9NQ03
ENSG00000270299
ENST00000488788.2
TSL:2
c.134-9994G>T
intron
N/AENSP00000474279.1S4R3F8
ENSG00000298442
ENST00000755524.1
n.179+3416C>A
intron
N/A

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1352808
Hom.:
0
Cov.:
33
AF XY:
0.00
AC XY:
0
AN XY:
669720
African (AFR)
AF:
0.00
AC:
0
AN:
28728
American (AMR)
AF:
0.00
AC:
0
AN:
37310
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
23564
East Asian (EAS)
AF:
0.00
AC:
0
AN:
32382
South Asian (SAS)
AF:
0.00
AC:
0
AN:
75180
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
46986
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5206
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
1049090
Other (OTH)
AF:
0.00
AC:
0
AN:
54362
GnomAD4 genome
Cov.:
32

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
0.43
BayesDel_addAF
Benign
-0.23
T
BayesDel_noAF
Benign
-0.57
CADD
Uncertain
24
DANN
Uncertain
0.99
DEOGEN2
Benign
0.11
T
Eigen
Benign
-0.081
Eigen_PC
Benign
-0.075
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Benign
0.65
T
M_CAP
Benign
0.078
D
MetaRNN
Benign
0.21
T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
1.7
L
PhyloP100
4.8
PrimateAI
Pathogenic
0.92
D
PROVEAN
Benign
-2.2
N
REVEL
Benign
0.14
Sift
Benign
0.28
T
Sift4G
Benign
0.28
T
Polyphen
0.66
P
Vest4
0.27
MutPred
0.55
Gain of helix (P = 0.062)
MVP
0.055
MPC
1.7
ClinPred
0.80
D
GERP RS
3.2
Varity_R
0.19
gMVP
0.28
Mutation Taster
=70/30
polymorphism

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: rs1984078380; hg19: chr20-644958; API