NM_030962.4:c.55+19911A>C

Variant names:

• chr11-10274104-T-G
• rs11042714
• NM_030962.4:c.55+19911A>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.55+19911A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.46 in 152,040 control chromosomes in the GnomAD database, including 16,905 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 (16905 hom., cov: 32)
• Consequence: SBF2 NM_030962.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.332
• Publications: 8 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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.537 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SBF2	NM_030962.4	MANE Select	c.55+19911A>C		intron	N/A	NP_112224.1
	SBF2	NM_001386339.1		c.55+19911A>C		intron	N/A	NP_001373268.1
	SBF2	NM_001424318.1		c.91+26302A>C		intron	N/A	NP_001411247.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SBF2	ENST00000256190.13	TSL:1 MANE Select	c.55+19911A>C		intron	N/A	ENSP00000256190.8
	SBF2	ENST00000533770.6	TSL:1	c.55+19911A>C		intron	N/A	ENSP00000509247.1
	SBF2	ENST00000526353.2	TSL:1	n.205+19911A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.459 AC: 69791 AN: 151922 Hom.: 16884 Cov.: 32

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.438

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.460 AC: 69865 AN: 152040 Hom.: 16905 Cov.: 32 AF XY: 0.460 AC XY: 34199 AN XY: 74286

African (AFR) AF: 0.311 AC: 12880 AN: 41476

American (AMR) AF: 0.471 AC: 7199 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 1707 AN: 3468

East Asian (EAS) AF: 0.339 AC: 1754 AN: 5168

South Asian (SAS) AF: 0.482 AC: 2317 AN: 4812

European-Finnish (FIN) AF: 0.543 AC: 5719 AN: 10534

Middle Eastern (MID) AF: 0.438 AC: 128 AN: 292

European-Non Finnish (NFE) AF: 0.541 AC: 36804 AN: 67988

Other (OTH) AF: 0.454 AC: 959 AN: 2114

Alfa AF: 0.499 Hom.: 8099

Bravo AF: 0.442

Asia WGS AF: 0.376 AC: 1308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.3
DANN	Benign	0.71
PhyloP100		0.33
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: rs11042714; hg19: chr11-10295651;