rs11042617

Variant names:

• chr11-10086937-G-A
• rs11042617
• NM_030962.4:c.142-43956C>T

Your query was ambiguous. Multiple possible variants found:

• chr11-10086937-G-A
• chr11-10086937-G-T

Variant summary

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

The NM_030962.4(SBF2):​c.142-43956C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.453 in 151,996 control chromosomes in the GnomAD database, including 16,072 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 0.45 (16072 hom., cov: 32)
• Consequence: SBF2 NM_030962.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0770
• Publications: 10 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 (AMR) allele frequency at 95% confidence interval = 0.547 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SBF2	NM_030962.4	c.142-43956C>T		intron_variant	Intron 2 of 39	ENST00000256190.13	NP_112224.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SBF2	ENST00000256190.13	c.142-43956C>T		intron_variant	Intron 2 of 39	1	NM_030962.4	ENSP00000256190.8

Frequencies

GnomAD3 genomes AF: 0.453 AC: 68760 AN: 151878 Hom.: 16054 Cov.: 32

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.453 AC: 68827 AN: 151996 Hom.: 16072 Cov.: 32 AF XY: 0.456 AC XY: 33876 AN XY: 74266

African (AFR) AF: 0.357 AC: 14779 AN: 41450

American (AMR) AF: 0.557 AC: 8502 AN: 15276

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

East Asian (EAS) AF: 0.478 AC: 2474 AN: 5174

South Asian (SAS) AF: 0.417 AC: 2007 AN: 4812

European-Finnish (FIN) AF: 0.522 AC: 5510 AN: 10550

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.485 AC: 32966 AN: 67954

Other (OTH) AF: 0.424 AC: 895 AN: 2112

Alfa AF: 0.460 Hom.: 20043

Bravo AF: 0.453

Asia WGS AF: 0.420 AC: 1459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.82
DANN	Benign	0.33
PhyloP100		-0.077
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: rs11042617; hg19: chr11-10108484;