Variant rs4927095 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000610401.6(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
ENST00000610401.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.494

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 made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SSBP3	NM_145716.4 linkuse as main transcript	c.276+44919G>C		intron_variant		ENST00000610401.6	NP_663768.1
SSBP3	NM_001394365.1 linkuse as main transcript	c.-55+56414G>C		intron_variant			NP_001381294.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SSBP3	ENST00000610401.6 linkuse as main transcript	c.276+44919G>C		intron_variant		5	NM_145716.4	ENSP00000479674	P1	Q9BWW4-1

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

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.227

GnomAD4 genome

AF:

0.124

AC:

18846

AN:

152246

Hom.:

1742

Cov.:

AF XY:

0.128

AC XY:

9515

AN XY:

74424

show subpopulations

Gnomad4 AFR

AF:

0.0283

Gnomad4 AMR

AF:

0.137

Gnomad4 ASJ

AF:

0.0815

Gnomad4 EAS

AF:

0.359

Gnomad4 SAS

AF:

0.384

Gnomad4 FIN

AF:

0.107

Gnomad4 NFE

AF:

0.147

Gnomad4 OTH

AF:

0.142

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

2.1

DANN

Benign

0.38

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over