rs780382

Variant names:

• chr11-9859928-A-G
• rs780382
• NM_030962.4:c.1930-1532T>C

Your query was ambiguous. Multiple possible variants found:

• chr11-9859928-A-G
• chr11-9859928-A-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.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
• Publications: 2 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

ENSG00000255476 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SBF2	NM_030962.4	c.1930-1532T>C		intron_variant	Intron 17 of 39	ENST00000256190.13	NP_112224.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SBF2	ENST00000256190.13	c.1930-1532T>C		intron_variant	Intron 17 of 39	1	NM_030962.4	ENSP00000256190.8

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

African (AFR) AF: 0.681 AC: 28233 AN: 41480

American (AMR) AF: 0.652 AC: 9966 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.642 AC: 2228 AN: 3470

East Asian (EAS) AF: 0.603 AC: 3114 AN: 5164

South Asian (SAS) AF: 0.622 AC: 2996 AN: 4818

European-Finnish (FIN) AF: 0.571 AC: 6024 AN: 10544

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.599 AC: 40727 AN: 67964

Other (OTH) AF: 0.615 AC: 1301 AN: 2114

Alfa AF: 0.609 Hom.: 121373

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
PhyloP100		-1.0
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: rs780382; hg19: chr11-9881475;