GeneBe

NM_032627.5:c.57G>A

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7

The NM_032627.5(SSBP4):​c.57G>A​(p.Glu19Glu) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000975 in 1,025,682 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 31)
Exomes 𝑓: 9.7e-7 ( 0 hom. )

Consequence

SSBP4
NM_032627.5 splice_region, synonymous

Scores

1
1
Splicing: ADA: 0.05398
2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.630
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 was made for transcript

Our verdict: Likely_benign. The variant received -1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.24).
BP7
Synonymous conserved (PhyloP=0.63 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SSBP4NM_032627.5 linkc.57G>A p.Glu19Glu splice_region_variant, synonymous_variant Exon 1 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.57G>A p.Glu19Glu splice_region_variant, synonymous_variant Exon 1 of 18 1 NM_032627.5 ENSP00000270061.5 Q9BWG4-1

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
AF:
9.75e-7
AC:
1
AN:
1025682
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
487614
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
20282
American (AMR)
AF:
0.00
AC:
0
AN:
6114
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
11016
East Asian (EAS)
AF:
0.00
AC:
0
AN:
19616
South Asian (SAS)
AF:
0.00
AC:
0
AN:
24198
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
19310
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
3508
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
882960
Other (OTH)
AF:
0.0000259
AC:
1
AN:
38678
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.24
CADD
Benign
17
DANN
Uncertain
0.98
PhyloP100
0.63
PromoterAI
-0.15
Neutral

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
0.054
dbscSNV1_RF
Benign
0.31
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

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Other links and lift over

dbSNP: rs2144667403; hg19: chr19-18530515; API