rs10500712

Positions:

• chr11-9881250-G-A

Variant summary

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

The NM_030962.4(SBF2):​c.1929+14693C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.092 in 152,218 control chromosomes in the GnomAD database, including 705 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 0.092 (705 hom., cov: 32)
• Consequence: SBF2 NM_030962.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0880

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SBF2	NM_030962.4	c.1929+14693C>T		intron_variant		ENST00000256190.13
LOC101928008	NR_120539.1	n.136-34356G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SBF2	ENST00000256190.13	c.1929+14693C>T		intron_variant		1	NM_030962.4	P3
	ENST00000533659.1	n.135-34356G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0921 AC: 14005 AN: 152100 Hom.: 705 Cov.: 32

Gnomad AFR AF: 0.0548

Gnomad AMI AF: 0.0967

Gnomad AMR AF: 0.0783

Gnomad ASJ AF: 0.0847

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.0993

Gnomad MID AF: 0.0701

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.0847

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

GnomAD4 genome AF: 0.0920 AC: 14008 AN: 152218 Hom.: 705 Cov.: 32 AF XY: 0.0916 AC XY: 6813 AN XY: 74406

Gnomad4 AFR AF: 0.0547

Gnomad4 AMR AF: 0.0782

Gnomad4 ASJ AF: 0.0847

Gnomad4 EAS AF: 0.191

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.0993

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.0881

Alfa AF: 0.101 Hom.: 491

Bravo AF: 0.0894

Asia WGS AF: 0.154 AC: 535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
DANN	Benign	0.41

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: rs10500712; hg19: chr11-9902797;