rs11042725

Positions:

• chr11-10303778-C-A
• chr11-10303778-C-G

Variant summary

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

The NM_001424318.1(SBF2):​c.-485G>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 152,172 control chromosomes in the GnomAD database, including 13,336 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 0.41 (13323 hom., cov: 33)
  • Exomes 𝑓: 0.48 (13 hom.)
• Consequence: SBF2 NM_001424318.1 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.349

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SBF2	NM_001424318.1	c.-485G>T		5_prime_UTR_premature_start_codon_gain_variant	1/41		NP_001411247.1
SBF2	NM_001424318.1	c.-485G>T		5_prime_UTR_variant	1/41		NP_001411247.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SBF2	ENST00000685217.1	n.386+714G>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.408 AC: 61972 AN: 151958 Hom.: 13309 Cov.: 33

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.396

GnomAD4 exome AF: 0.479 AC: 46 AN: 96 Hom.: 13 AF XY: 0.469 AC XY: 30 AN XY: 64

Gnomad4 AMR exome AF: 0.500

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.515

Gnomad4 OTH exome AF: 0.300

GnomAD4 genome AF: 0.408 AC: 62029 AN: 152076 Hom.: 13323 Cov.: 33 AF XY: 0.409 AC XY: 30379 AN XY: 74336

Gnomad4 AFR AF: 0.301

Gnomad4 AMR AF: 0.428

Gnomad4 ASJ AF: 0.389

Gnomad4 EAS AF: 0.275

Gnomad4 SAS AF: 0.322

Gnomad4 FIN AF: 0.504

Gnomad4 NFE AF: 0.473

Gnomad4 OTH AF: 0.391

Alfa AF: 0.401 Hom.: 3075

Bravo AF: 0.395

Asia WGS AF: 0.257 AC: 893 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.8
DANN	Benign	0.46

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11042725; hg19: chr11-10325325;