rs11042617

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
SBF2	NM_030962.4	c.142-43956C>T		intron_variant		ENST00000256190.13	NP_112224.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SBF2	ENST00000256190.13	c.142-43956C>T		intron_variant		1	NM_030962.4	ENSP00000256190	P3

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

Gnomad4 AFR AF: 0.357

Gnomad4 AMR AF: 0.557

Gnomad4 ASJ AF: 0.382

Gnomad4 EAS AF: 0.478

Gnomad4 SAS AF: 0.417

Gnomad4 FIN AF: 0.522

Gnomad4 NFE AF: 0.485

Gnomad4 OTH AF: 0.424

Alfa AF: 0.460 Hom.: 14979

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs11042617; hg19: chr11-10108484;