chr5-81437440-C-G

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_001256732.3(SSBP2):​c.971G>C​(p.Ser324Thr) 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)

Consequence

SSBP2
NM_001256732.3 missense

Scores

1
7
11

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 7.13
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]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.27763158).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SSBP2NM_001256732.3 linkc.971G>C p.Ser324Thr missense_variant Exon 15 of 17 ENST00000615665.5 NP_001243661.1 P81877A0A087X159

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SSBP2ENST00000615665.5 linkc.971G>C p.Ser324Thr missense_variant Exon 15 of 17 5 NM_001256732.3 ENSP00000483921.1 A0A087X159

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
29
GnomAD4 genome
Cov.:
32

ClinVar

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

Submissions by phenotype

not provided Uncertain:1
Oct 21, 2019
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.094
BayesDel_addAF
Uncertain
0.040
T
BayesDel_noAF
Benign
-0.18
CADD
Uncertain
23
DANN
Uncertain
0.99
DEOGEN2
Benign
0.25
T;T;.;.;T;.;.
Eigen
Uncertain
0.34
Eigen_PC
Uncertain
0.47
FATHMM_MKL
Pathogenic
0.99
D
LIST_S2
Benign
0.85
D;D;T;D;D;D;D
M_CAP
Benign
0.0067
T
MetaRNN
Benign
0.28
T;T;T;T;T;T;T
MetaSVM
Benign
-0.73
T
MutationAssessor
Benign
0.63
N;.;.;.;.;.;.
PrimateAI
Uncertain
0.74
T
PROVEAN
Benign
-1.8
N;.;N;N;N;N;N
REVEL
Benign
0.15
Sift
Uncertain
0.0050
D;.;D;D;D;D;D
Sift4G
Uncertain
0.013
D;D;T;D;D;D;D
Polyphen
0.79
P;.;.;.;.;.;.
Vest4
0.43
MutPred
0.12
Loss of phosphorylation at S316 (P = 0.0597);.;.;.;.;.;.;
MVP
0.10
MPC
0.78
ClinPred
0.90
D
GERP RS
5.5
Varity_R
0.49
gMVP
0.56

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: rs1762742193; hg19: chr5-80733259; API