Variant rs56853707 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The ENST00000380817.8(SBF1):c.5452-13_5452-12del variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 1,610,878 control chromosomes in the GnomAD database, including 139,826 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.37 ( 12051 hom., cov: 0)

Exomes 𝑓: 0.41 ( 127775 hom. )

Consequence

SBF1
ENST00000380817.8 splice_polypyrimidine_tract, intron

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -1.13

Variant links:

Genes affected

SBF1 (HGNC:10542): (SET binding factor 1) This gene encodes a member of the protein-tyrosine phosphatase family. However, the encoded protein does not appear to be a catalytically active phosphatase because it lacks several amino acids in the catalytic pocket. This protein contains a Guanine nucleotide exchange factor (GEF) domain which is necessary for its role in growth and differentiation. Mutations in this gene have been associated with Charcot-Marie-Tooth disease 4B3. Pseudogenes of this gene have been defined on chromosomes 1 and 8. [provided by RefSeq, Dec 2014]

SBF1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 22-50447464-CCA-C is Benign according to our data. Variant chr22-50447464-CCA-C is described in ClinVar as [Benign]. Clinvar id is 258880.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr22-50447464-CCA-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
SBF1	NM_002972.4 linkuse as main transcript	c.5452-13_5452-12del	splice_polypyrimidine_tract_variant, intron_variant	ENST00000380817.8	NP_002963.2
SBF1	NM_001365819.1 linkuse as main transcript	c.5377-13_5377-12del	splice_polypyrimidine_tract_variant, intron_variant		NP_001352748.1
SBF1	NM_001410794.1 linkuse as main transcript	c.5455-13_5455-12del	splice_polypyrimidine_tract_variant, intron_variant		NP_001397723.1
SBF1	NM_001410795.1 linkuse as main transcript	c.5374-13_5374-12del	splice_polypyrimidine_tract_variant, intron_variant		NP_001397724.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SBF1	ENST00000380817.8 linkuse as main transcript	c.5452-13_5452-12del		splice_polypyrimidine_tract_variant, intron_variant		1	NM_002972.4	ENSP00000370196	P3	O95248-5

Frequencies

GnomAD3 genomes

AF:

0.372

AC:

56387

AN:

151472

Hom.:

12050

Cov.:

show subpopulations

Gnomad AFR

AF:

0.175

Gnomad AMI

AF:

0.473

Gnomad AMR

AF:

0.445

Gnomad ASJ

AF:

0.473

Gnomad EAS

AF:

0.777

Gnomad SAS

AF:

0.330

Gnomad FIN

AF:

0.523

Gnomad MID

AF:

0.304

Gnomad NFE

AF:

0.419

Gnomad OTH

AF:

0.403

GnomAD3 exomes

AF:

0.437

AC:

108803

AN:

249114

Hom.:

26063

AF XY:

0.431

AC XY:

58284

AN XY:

135160

show subpopulations

Gnomad AFR exome

AF:

0.164

Gnomad AMR exome

AF:

0.511

Gnomad ASJ exome

AF:

0.478

Gnomad EAS exome

AF:

0.781

Gnomad SAS exome

AF:

0.318

Gnomad FIN exome

AF:

0.516

Gnomad NFE exome

AF:

0.411

Gnomad OTH exome

AF:

0.428

GnomAD4 exome

AF:

0.410

AC:

597967

AN:

1459288

Hom.:

127775

AF XY:

0.408

AC XY:

296392

AN XY:

725948

show subpopulations

Gnomad4 AFR exome

AF:

0.159

Gnomad4 AMR exome

AF:

0.504

Gnomad4 ASJ exome

AF:

0.483

Gnomad4 EAS exome

AF:

0.744

Gnomad4 SAS exome

AF:

0.323

Gnomad4 FIN exome

AF:

0.512

Gnomad4 NFE exome

AF:

0.402

Gnomad4 OTH exome

AF:

0.406

GnomAD4 genome

AF:

0.372

AC:

56402

AN:

151590

Hom.:

12051

Cov.:

AF XY:

0.380

AC XY:

28109

AN XY:

74012

show subpopulations

Gnomad4 AFR

AF:

0.175

Gnomad4 AMR

AF:

0.445

Gnomad4 ASJ

AF:

0.473

Gnomad4 EAS

AF:

0.776

Gnomad4 SAS

AF:

0.331

Gnomad4 FIN

AF:

0.523

Gnomad4 NFE

AF:

0.419

Gnomad4 OTH

AF:

0.400

Alfa

AF:

0.415

Hom.:

2488

Bravo

AF:

0.365

Asia WGS

AF:

0.446

AC:

1549

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 15, 2018	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.13

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over