dbSNP rs4927095: SSBP3:c.276+44919G>C (chr1-54356942-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_145716.4(SSBP3):c.276+44919G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 152,320 control chromosomes in the GnomAD database, including 1,745 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.12 ( 1742 hom., cov: 32)

Exomes 𝑓: 0.20 ( 3 hom. )

Consequence

SSBP3
NM_145716.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.494

Publications

1 publications found

Variant links:

Genes affected

SSBP3 (HGNC:15674): (single stranded DNA binding protein 3) Predicted to enable single-stranded DNA binding activity and transcription coactivator activity. Predicted to be involved in head development and positive regulation of transcription by RNA polymerase II. Predicted to act upstream of or within hematopoietic progenitor cell differentiation. Predicted to be part of protein-containing complex. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

SSBP3 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_145716.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SSBP3	NM_145716.4	MANE Select	c.276+44919G>C	intron	N/A	NP_663768.1
SSBP3	NM_001394360.1		c.276+44919G>C	intron	N/A	NP_001381289.1
SSBP3	NM_018070.5		c.276+44919G>C	intron	N/A	NP_060540.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SSBP3	ENST00000610401.6	TSL:5 MANE Select	c.276+44919G>C	intron	N/A	ENSP00000479674.2
SSBP3	ENST00000357475.9	TSL:1	c.276+44919G>C	intron	N/A	ENSP00000350067.4
SSBP3	ENST00000371320.8	TSL:1	n.549+44919G>C	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.124

AC:

18840

AN:

152128

Hom.:

1737

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0284

Gnomad AMI

AF:

0.117

Gnomad AMR

AF:

0.136

Gnomad ASJ

AF:

0.0815

Gnomad EAS

AF:

0.359

Gnomad SAS

AF:

0.384

Gnomad FIN

AF:

0.107

Gnomad MID

AF:

0.127

Gnomad NFE

AF:

0.147

Gnomad OTH

AF:

0.138

GnomAD4 exome

AF:

0.203

AC:

AN:

Hom.:

AF XY:

0.220

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.227

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.431

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.124

AC:

18846

AN:

152246

Hom.:

1742

Cov.:

AF XY:

0.128

AC XY:

9515

AN XY:

74424

show subpopulations

African (AFR)

AF:

0.0283

AC:

1176

AN:

41574

American (AMR)

AF:

0.137

AC:

2088

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.0815

AC:

283

AN:

3472

East Asian (EAS)

AF:

0.359

AC:

1858

AN:

5178

South Asian (SAS)

AF:

0.384

AC:

1847

AN:

4810

European-Finnish (FIN)

AF:

0.107

AC:

1137

AN:

10590

Middle Eastern (MID)

AF:

0.127

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.147

AC:

10014

AN:

68016

Other (OTH)

AF:

0.142

AC:

299

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

809

1619

2428

3238

4047

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

232

464

696

928

1160

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.132

Hom.:

187

Bravo

AF:

0.119

Asia WGS

AF:

0.355

AC:

1233

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

2.1

(source)

DANN

Benign

0.38

PhyloP100

-0.49

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over