rs780382

chr11-9859928-A-Gchr11-9859928-A-T

Variant summary

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

The NM_030962.4(SBF2):c.1930-1532T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.626 in 152,042 control chromosomes in the GnomAD database, including 29,966 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 0.63 (29966 hom., cov: 32)
• Consequence: SBF2 NM_030962.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.674 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SBF2	NM_030962.4	c.1930-1532T>C		intron_variant		ENST00000256190.13
LOC101928008	NR_120539.1	n.135+20652A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SBF2	ENST00000256190.13	c.1930-1532T>C		intron_variant		1	NM_030962.4	P3
	ENST00000533659.1	n.134+20652A>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.626 AC: 95159 AN: 151924 Hom.: 29947 Cov.: 32

Gnomad AFR AF: 0.681

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.604

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.626 AC: 95217 AN: 152042 Hom.: 29966 Cov.: 32 AF XY: 0.625 AC XY: 46450 AN XY: 74300

Gnomad4 AFR AF: 0.681

Gnomad4 AMR AF: 0.652

Gnomad4 ASJ AF: 0.642

Gnomad4 EAS AF: 0.603

Gnomad4 SAS AF: 0.622

Gnomad4 FIN AF: 0.571

Gnomad4 NFE AF: 0.599

Gnomad4 OTH AF: 0.615

Alfa AF: 0.607 Hom.: 56690

Bravo AF: 0.636

Asia WGS AF: 0.591 AC: 2055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.37
Dann	Benign	0.44

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: rs780382; hg19: chr11-9881475;