rs12362504

Positions:

• chr11-9907995-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.1861-11984A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 152,082 control chromosomes in the GnomAD database, including 11,089 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 0.37 (11089 hom., cov: 33)
• Consequence: SBF2 NM_030962.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.353

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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.527 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SBF2	NM_030962.4	c.1861-11984A>G		intron_variant		ENST00000256190.13
LOC101928008	NR_120539.1	n.136-7611T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SBF2	ENST00000256190.13	c.1861-11984A>G		intron_variant		1	NM_030962.4	P3
	ENST00000533659.1	n.135-7611T>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.366 AC: 55626 AN: 151962 Hom.: 11077 Cov.: 33

Gnomad AFR AF: 0.534

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.366 AC: 55667 AN: 152082 Hom.: 11089 Cov.: 33 AF XY: 0.365 AC XY: 27160 AN XY: 74346

Gnomad4 AFR AF: 0.533

Gnomad4 AMR AF: 0.336

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.267

Gnomad4 SAS AF: 0.303

Gnomad4 FIN AF: 0.331

Gnomad4 NFE AF: 0.287

Gnomad4 OTH AF: 0.368

Alfa AF: 0.318 Hom.: 1615

Bravo AF: 0.380

Asia WGS AF: 0.298 AC: 1034 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.1
DANN	Benign	0.71

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: rs12362504; hg19: chr11-9929542;