rs9332432

Variant names:

• chr11-9917938-A-G
• rs9332432
• NM_030962.4:c.1861-21927T>C

Variant summary

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

The NM_030962.4(SBF2):​c.1861-21927T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.584 in 151,112 control chromosomes in the GnomAD database, including 26,425 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 0.58 (26425 hom., cov: 30)
• Consequence: SBF2 NM_030962.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.213
• Publications: 2 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: Orphanet, Labcorp Genetics (formerly Invitae), G2P, ClinGen, Ambry Genetics

ENSG00000255476 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.643 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.1861-21927T>C		intron	N/A	NP_112224.1
	SBF2	NM_001386339.1		c.1861-21927T>C		intron	N/A	NP_001373268.1
	SBF2	NM_001424318.1		c.1897-21927T>C		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.1861-21927T>C		intron	N/A	ENSP00000256190.8
	SBF2	ENST00000533770.6	TSL:1	c.1861-21927T>C		intron	N/A	ENSP00000509247.1
	ENSG00000255476	ENST00000533659.1	TSL:1	n.212+2255A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.585 AC: 88266 AN: 150994 Hom.: 26410 Cov.: 30

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.613

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.565

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

GnomAD4 genome AF: 0.584 AC: 88317 AN: 151112 Hom.: 26425 Cov.: 30 AF XY: 0.582 AC XY: 43023 AN XY: 73886

African (AFR) AF: 0.650 AC: 26456 AN: 40704

American (AMR) AF: 0.565 AC: 8583 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.613 AC: 2127 AN: 3470

East Asian (EAS) AF: 0.301 AC: 1551 AN: 5156

South Asian (SAS) AF: 0.542 AC: 2610 AN: 4812

European-Finnish (FIN) AF: 0.564 AC: 5939 AN: 10538

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.579 AC: 39307 AN: 67944

Other (OTH) AF: 0.561 AC: 1178 AN: 2098

Alfa AF: 0.582 Hom.: 5261

Bravo AF: 0.588

Asia WGS AF: 0.405 AC: 1406 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.7
DANN	Benign	0.63
PhyloP100		0.21
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: rs9332432; hg19: chr11-9939485;