NM_030962.4:c.142-8321C>G

Variant names:

• chr11-10051302-G-C
• rs12288355
• NM_030962.4:c.142-8321C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_030962.4(SBF2):​c.142-8321C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.462 in 151,766 control chromosomes in the GnomAD database, including 16,566 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 0.46 (16566 hom., cov: 32)
• Consequence: SBF2 NM_030962.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.136
• Publications: 3 publications found

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 Gene-Disease associations (from GenCC):

• Charcot-Marie-Tooth disease type 4B2

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), ClinGen, PanelApp Australia, Ambry Genetics, G2P, Orphanet

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030962.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SBF2	NM_030962.4	MANE Select	c.142-8321C>G		intron	N/A	NP_112224.1	Q86WG5-1
	SBF2	NM_001386339.1		c.142-8321C>G		intron	N/A	NP_001373268.1	A0A8I5KQ02
	SBF2	NM_001424318.1		c.178-8321C>G		intron	N/A	NP_001411247.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SBF2	ENST00000256190.13	TSL:1 MANE Select	c.142-8321C>G		intron	N/A	ENSP00000256190.8	Q86WG5-1
	SBF2	ENST00000533770.6	TSL:1	c.142-8321C>G		intron	N/A	ENSP00000509247.1	Q86WG5-3
	SBF2	ENST00000526353.2	TSL:1	n.292-8321C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.462 AC: 70006 AN: 151646 Hom.: 16547 Cov.: 32

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.322

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.462 AC: 70073 AN: 151766 Hom.: 16566 Cov.: 32 AF XY: 0.465 AC XY: 34488 AN XY: 74156

African (AFR) AF: 0.386 AC: 15998 AN: 41400

American (AMR) AF: 0.561 AC: 8555 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1323 AN: 3464

East Asian (EAS) AF: 0.478 AC: 2475 AN: 5174

South Asian (SAS) AF: 0.418 AC: 2016 AN: 4822

European-Finnish (FIN) AF: 0.524 AC: 5518 AN: 10522

Middle Eastern (MID) AF: 0.332 AC: 97 AN: 292

European-Non Finnish (NFE) AF: 0.485 AC: 32911 AN: 67834

Other (OTH) AF: 0.430 AC: 906 AN: 2108

Alfa AF: 0.324 Hom.: 812

Bravo AF: 0.463

Asia WGS AF: 0.421 AC: 1454 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.6
DANN	Benign	0.40
PhyloP100		-0.14
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12288355; hg19: chr11-10072849;