rs6484147

Positions:

• chr11-10273556-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.55+20459A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.491 in 152,080 control chromosomes in the GnomAD database, including 18,713 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 0.49 (18713 hom., cov: 32)
• Consequence: SBF2 NM_030962.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.322

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SBF2	NM_030962.4	c.55+20459A>G		intron_variant		ENST00000256190.13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SBF2	ENST00000256190.13	c.55+20459A>G		intron_variant		1	NM_030962.4	P3

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74615 AN: 151962 Hom.: 18682 Cov.: 32

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.491 AC: 74709 AN: 152080 Hom.: 18713 Cov.: 32 AF XY: 0.491 AC XY: 36501 AN XY: 74334

Gnomad4 AFR AF: 0.412

Gnomad4 AMR AF: 0.490

Gnomad4 ASJ AF: 0.522

Gnomad4 EAS AF: 0.339

Gnomad4 SAS AF: 0.480

Gnomad4 FIN AF: 0.542

Gnomad4 NFE AF: 0.544

Gnomad4 OTH AF: 0.488

Alfa AF: 0.507 Hom.: 3394

Bravo AF: 0.479

Asia WGS AF: 0.382 AC: 1330 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.58

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: rs6484147; hg19: chr11-10295103;