rs1372809

Positions:

• chr11-10222558-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000256190.13(SBF2):​c.56-28571G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.393 in 151,988 control chromosomes in the GnomAD database, including 12,827 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 0.39 (12827 hom., cov: 31)
• Consequence: SBF2 ENST00000256190.13 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.172

Genes affected

SBF2 (HGNC:2135): (SET binding factor 2) This gene encodes a pseudophosphatase and member of the myotubularin-related protein family. This gene maps within the CMT4B2 candidate region of chromosome 11p15 and mutations in this gene have been associated with Charcot-Marie-Tooth Disease, type 4B2. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SBF2	NM_030962.4	c.56-28571G>C		intron_variant		ENST00000256190.13	NP_112224.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SBF2	ENST00000256190.13	c.56-28571G>C		intron_variant		1	NM_030962.4	ENSP00000256190	P3

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59734 AN: 151870 Hom.: 12807 Cov.: 31

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.0543

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.380

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.393 AC: 59801 AN: 151988 Hom.: 12827 Cov.: 31 AF XY: 0.394 AC XY: 29278 AN XY: 74282

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.358

Gnomad4 ASJ AF: 0.439

Gnomad4 EAS AF: 0.0545

Gnomad4 SAS AF: 0.428

Gnomad4 FIN AF: 0.510

Gnomad4 NFE AF: 0.482

Gnomad4 OTH AF: 0.383

Alfa AF: 0.439 Hom.: 1919

Bravo AF: 0.369

Asia WGS AF: 0.229 AC: 798 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	3.0
DANN	Benign	0.74

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

Other links and lift over

dbSNP: rs1372809; hg19: chr11-10244105; COSMIC: COSV56312698;