11-10074693-C-T

Variant names:

• chr11-10074693-C-T
• rs7119000
• NM_030962.4:c.142-31712G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_030962.4(SBF2):​c.142-31712G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 151,944 control chromosomes in the GnomAD database, including 16,645 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 0.46 (16645 hom., cov: 32)
• Consequence: SBF2 NM_030962.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.438
• Publications: 8 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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.552 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SBF2	NM_030962.4	c.142-31712G>A		intron_variant	Intron 2 of 39	ENST00000256190.13	NP_112224.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SBF2	ENST00000256190.13	c.142-31712G>A		intron_variant	Intron 2 of 39	1	NM_030962.4	ENSP00000256190.8

Frequencies

GnomAD3 genomes AF: 0.462 AC: 70212 AN: 151824 Hom.: 16626 Cov.: 32

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.463 AC: 70279 AN: 151944 Hom.: 16645 Cov.: 32 AF XY: 0.466 AC XY: 34582 AN XY: 74258

African (AFR) AF: 0.389 AC: 16110 AN: 41426

American (AMR) AF: 0.562 AC: 8571 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1319 AN: 3462

East Asian (EAS) AF: 0.482 AC: 2488 AN: 5162

South Asian (SAS) AF: 0.418 AC: 2011 AN: 4810

European-Finnish (FIN) AF: 0.523 AC: 5516 AN: 10556

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.485 AC: 32981 AN: 67944

Other (OTH) AF: 0.430 AC: 910 AN: 2116

Alfa AF: 0.374 Hom.: 1530

Bravo AF: 0.464

Asia WGS AF: 0.421 AC: 1455 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.42
DANN	Benign	0.19
PhyloP100		-0.44
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: rs7119000; hg19: chr11-10096240;