5-81751009-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001256732.3(SSBP2):​c.34G>A​(p.Val12Ile) variant causes a missense change. The variant allele was found at a frequency of 0.000000691 in 1,447,064 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 31)
Exomes 𝑓: 6.9e-7 ( 0 hom. )

Consequence

SSBP2
NM_001256732.3 missense

Scores

1
6
12

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.05
Variant links:
Genes affected
SSBP2 (HGNC:15831): (single stranded DNA binding protein 2) This gene encodes a subunit of a protein complex that interacts with single-stranded DNA and is involved in the DNA damage response and maintenance of genome stability. The encoded protein may also play a role in telomere repair. A variant of this gene may be associated with survival in human glioblastoma patients. [provided by RefSeq, Sep 2016]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.11406919).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SSBP2NM_001256732.3 linkc.34G>A p.Val12Ile missense_variant Exon 1 of 17 ENST00000615665.5 NP_001243661.1 P81877A0A087X159

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SSBP2ENST00000615665.5 linkc.34G>A p.Val12Ile missense_variant Exon 1 of 17 5 NM_001256732.3 ENSP00000483921.1 A0A087X159

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
AF:
6.91e-7
AC:
1
AN:
1447064
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
718390
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000120
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
31

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Aug 12, 2021
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.34G>A (p.V12I) alteration is located in exon 1 (coding exon 1) of the SSBP2 gene. This alteration results from a G to A substitution at nucleotide position 34, causing the valine (V) at amino acid position 12 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.37
BayesDel_addAF
Benign
-0.11
T
BayesDel_noAF
Benign
-0.40
CADD
Uncertain
24
DANN
Uncertain
1.0
DEOGEN2
Benign
0.32
T;T;.;.;.;.
Eigen
Benign
-0.18
Eigen_PC
Benign
-0.054
FATHMM_MKL
Uncertain
0.94
D
LIST_S2
Uncertain
0.90
D;D;D;D;D;D
M_CAP
Uncertain
0.21
D
MetaRNN
Benign
0.11
T;T;T;T;T;T
MetaSVM
Benign
-0.84
T
MutationAssessor
Benign
0.69
N;.;N;N;N;N
PrimateAI
Pathogenic
0.85
D
PROVEAN
Benign
-0.73
N;.;N;N;N;N
REVEL
Benign
0.088
Sift
Uncertain
0.025
D;.;D;D;D;D
Sift4G
Benign
0.20
T;T;T;T;T;T
Polyphen
0.0020
B;.;.;.;.;.
Vest4
0.15
MutPred
0.085
Loss of MoRF binding (P = 0.1643);Loss of MoRF binding (P = 0.1643);Loss of MoRF binding (P = 0.1643);Loss of MoRF binding (P = 0.1643);Loss of MoRF binding (P = 0.1643);Loss of MoRF binding (P = 0.1643);
MVP
0.082
MPC
0.70
ClinPred
0.48
T
GERP RS
3.7
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
2.7
Varity_R
0.35
gMVP
0.39

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs757708024; hg19: chr5-81046828; API