rs535525251

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_032627.5(SSBP4):​c.353C>A​(p.Ala118Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,460,350 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. A118V) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 34)
Exomes 𝑓: 6.8e-7 ( 0 hom. )

Consequence

SSBP4
NM_032627.5 missense

Scores

8
11

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.74
Variant links:
Genes affected
SSBP4 (HGNC:15676): (single stranded DNA binding protein 4) Predicted to enable single-stranded DNA binding activity. Predicted to be involved in positive regulation of transcription by RNA polymerase II. Predicted to be integral component of membrane. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

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

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SSBP4NM_032627.5 linkc.353C>A p.Ala118Glu missense_variant Exon 5 of 18 ENST00000270061.12 NP_116016.1 Q9BWG4-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SSBP4ENST00000270061.12 linkc.353C>A p.Ala118Glu missense_variant Exon 5 of 18 1 NM_032627.5 ENSP00000270061.5 Q9BWG4-1

Frequencies

GnomAD3 genomes
Cov.:
34
GnomAD4 exome
AF:
6.85e-7
AC:
1
AN:
1460350
Hom.:
0
Cov.:
33
AF XY:
0.00000138
AC XY:
1
AN XY:
726542
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:
0.0000116
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.26
BayesDel_addAF
Benign
0.0061
T
BayesDel_noAF
Benign
-0.23
CADD
Benign
22
DANN
Uncertain
0.99
DEOGEN2
Benign
0.019
T;.;T;.;.
Eigen
Benign
0.10
Eigen_PC
Benign
0.010
FATHMM_MKL
Uncertain
0.86
D
LIST_S2
Uncertain
0.93
D;D;D;T;T
M_CAP
Benign
0.035
D
MetaRNN
Uncertain
0.59
D;D;D;D;D
MetaSVM
Benign
-0.68
T
MutationAssessor
Benign
1.6
.;L;L;.;.
PrimateAI
Uncertain
0.56
T
PROVEAN
Benign
-0.97
.;N;N;.;.
REVEL
Uncertain
0.38
Sift
Uncertain
0.0030
.;D;D;.;.
Sift4G
Uncertain
0.051
T;T;T;T;T
Polyphen
0.90
.;.;P;.;.
Vest4
0.50, 0.55
MutPred
0.57
.;Gain of phosphorylation at S116 (P = 0.1501);Gain of phosphorylation at S116 (P = 0.1501);.;.;
MVP
0.043
MPC
0.81
ClinPred
0.90
D
GERP RS
2.8
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.0
Varity_R
0.26
gMVP
0.33

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr19-18541724; API