rs716803

Positions:

• chr11-10225736-C-A
• chr11-10225736-C-T

Variant summary

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

The NM_030962.4(SBF2):​c.56-31749G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.49 in 151,664 control chromosomes in the GnomAD database, including 18,527 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 0.49 (18527 hom., cov: 32)
• Consequence: SBF2 NM_030962.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.523

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=-0.49).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.537 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SBF2	NM_030962.4	c.56-31749G>T		intron_variant		ENST00000256190.13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SBF2	ENST00000256190.13	c.56-31749G>T		intron_variant		1	NM_030962.4	P3

Frequencies

GnomAD3 genomes AF: 0.490 AC: 74207 AN: 151544 Hom.: 18496 Cov.: 32

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.490 AC: 74303 AN: 151664 Hom.: 18527 Cov.: 32 AF XY: 0.490 AC XY: 36299 AN XY: 74090

Gnomad4 AFR AF: 0.410

Gnomad4 AMR AF: 0.488

Gnomad4 ASJ AF: 0.519

Gnomad4 EAS AF: 0.340

Gnomad4 SAS AF: 0.476

Gnomad4 FIN AF: 0.552

Gnomad4 NFE AF: 0.541

Gnomad4 OTH AF: 0.485

Alfa AF: 0.370 Hom.: 997

Bravo AF: 0.477

Asia WGS AF: 0.381 AC: 1320 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	8.3
DANN	Benign	0.73

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: rs716803; hg19: chr11-10247283;