rs57153895

Positions:

• chr11-10301173-A-G

Variant summary

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

The ENST00000685217.1(SBF2):​n.386+3319T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 152,098 control chromosomes in the GnomAD database, including 13,004 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 0.40 (13004 hom., cov: 32)
• Consequence: SBF2 ENST00000685217.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0390

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SBF2	ENST00000685217.1	n.386+3319T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60807 AN: 151980 Hom.: 12996 Cov.: 32

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.400 AC: 60847 AN: 152098 Hom.: 13004 Cov.: 32 AF XY: 0.402 AC XY: 29880 AN XY: 74370

Gnomad4 AFR AF: 0.275

Gnomad4 AMR AF: 0.420

Gnomad4 ASJ AF: 0.361

Gnomad4 EAS AF: 0.282

Gnomad4 SAS AF: 0.326

Gnomad4 FIN AF: 0.516

Gnomad4 NFE AF: 0.472

Gnomad4 OTH AF: 0.375

Alfa AF: 0.415 Hom.: 1979

Bravo AF: 0.385

Asia WGS AF: 0.265 AC: 923 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.1
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs57153895; hg19: chr11-10322720;