rs7938647

chr11-10039876-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_030962.4(SBF2):c.279+2968A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 151,620 control chromosomes in the GnomAD database, including 3,975 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 0.20 (3975 hom., cov: 31)
• Consequence: SBF2 NM_030962.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.168

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=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.295 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SBF2	NM_030962.4	c.279+2968A>G		intron_variant		ENST00000256190.13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SBF2	ENST00000256190.13	c.279+2968A>G		intron_variant		1	NM_030962.4	P3

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30591 AN: 151502 Hom.: 3972 Cov.: 31

Gnomad AFR AF: 0.0603

Gnomad AMI AF: 0.176

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.00424

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.202 AC: 30604 AN: 151620 Hom.: 3975 Cov.: 31 AF XY: 0.199 AC XY: 14731 AN XY: 74144

Gnomad4 AFR AF: 0.0602

Gnomad4 AMR AF: 0.216

Gnomad4 ASJ AF: 0.208

Gnomad4 EAS AF: 0.00425

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.220

Gnomad4 NFE AF: 0.298

Gnomad4 OTH AF: 0.177

Alfa AF: 0.273 Hom.: 3431

Bravo AF: 0.191

Asia WGS AF: 0.0780 AC: 271 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
Cadd	Benign	5.8
Dann	Benign	0.86

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: rs7938647; hg19: chr11-10061423;