11-9889411-C-T

Variant names:

• chr11-9889411-C-T
• rs4910072
• NM_030962.4:c.1929+6532G>A

Variant summary

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

The NM_030962.4(SBF2):​c.1929+6532G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.843 in 152,186 control chromosomes in the GnomAD database, including 54,457 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 0.84 (54457 hom., cov: 32)
• Consequence: SBF2 NM_030962.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.363
• 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: Labcorp Genetics (formerly Invitae), ClinGen, PanelApp Australia, Ambry Genetics, G2P, Orphanet

ENSG00000255476 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.862 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.1929+6532G>A		intron	N/A	NP_112224.1	Q86WG5-1
	SBF2	NM_001386339.1		c.1929+6532G>A		intron	N/A	NP_001373268.1	A0A8I5KQ02
	SBF2	NM_001424318.1		c.1965+6532G>A		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.1929+6532G>A		intron	N/A	ENSP00000256190.8	Q86WG5-1
	SBF2	ENST00000533770.6	TSL:1	c.1929+6532G>A		intron	N/A	ENSP00000509247.1	Q86WG5-3
	ENSG00000255476	ENST00000533659.1	TSL:1	n.135-26195C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.843 AC: 128263 AN: 152068 Hom.: 54423 Cov.: 32

Gnomad AFR AF: 0.870

Gnomad AMI AF: 0.704

Gnomad AMR AF: 0.826

Gnomad ASJ AF: 0.876

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.891

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.857

Gnomad OTH AF: 0.843

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

GnomAD4 genome AF: 0.843 AC: 128344 AN: 152186 Hom.: 54457 Cov.: 32 AF XY: 0.840 AC XY: 62472 AN XY: 74412

African (AFR) AF: 0.870 AC: 36104 AN: 41504

American (AMR) AF: 0.826 AC: 12626 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.876 AC: 3043 AN: 3472

East Asian (EAS) AF: 0.536 AC: 2769 AN: 5170

South Asian (SAS) AF: 0.701 AC: 3380 AN: 4820

European-Finnish (FIN) AF: 0.891 AC: 9441 AN: 10600

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.857 AC: 58320 AN: 68016

Other (OTH) AF: 0.835 AC: 1766 AN: 2116

Alfa AF: 0.849 Hom.: 27605

Bravo AF: 0.839

Asia WGS AF: 0.597 AC: 2076 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.96
DANN	Benign	0.53
PhyloP100		-0.36
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: rs4910072; hg19: chr11-9910958;