11-10301931-A-G

Position:

• chr11-10301931-A-G

Variant summary

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

The NM_001424318.1(SBF2):​c.-3+1365T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 152,174 control chromosomes in the GnomAD database, including 6,518 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 0.27 (6518 hom., cov: 33)
• Consequence: SBF2 NM_001424318.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0440

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]

SBF2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SBF2	NM_001424318.1	c.-3+1365T>C		intron_variant			NP_001411247.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SBF2	ENST00000685217.1	n.386+2561T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41810 AN: 152056 Hom.: 6512 Cov.: 33

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.275 AC: 41831 AN: 152174 Hom.: 6518 Cov.: 33 AF XY: 0.273 AC XY: 20282 AN XY: 74400

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.330

Gnomad4 ASJ AF: 0.263

Gnomad4 EAS AF: 0.280

Gnomad4 SAS AF: 0.255

Gnomad4 FIN AF: 0.271

Gnomad4 NFE AF: 0.356

Gnomad4 OTH AF: 0.260

Alfa AF: 0.325 Hom.: 4236

Bravo AF: 0.270

Asia WGS AF: 0.217 AC: 754 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	5.4
DANN	Benign	0.69

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4399321; hg19: chr11-10323478;