Variant chr11-9778903-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_030962.4(SBF2):c.*1515G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 152,540 control chromosomes in the GnomAD database, including 9,206 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.33 ( 9160 hom., cov: 33)

Exomes 𝑓: 0.48 ( 46 hom. )

Consequence

SBF2
NM_030962.4 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.32

Variant links:

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 links:

SBF2-AS1 (HGNC:27438): (SBF2 antisense RNA 1)

SBF2-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.61).

BP6

Variant 11-9778903-C-T is Benign according to our data. Variant chr11-9778903-C-T is described in ClinVar as [Benign]. Clinvar id is 306552.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE
SBF2	NM_030962.4 linkuse as main transcript	c.*1515G>A	3_prime_UTR_variant	40/40	ENST00000256190.13
SBF2-AS1	NR_036485.1 linkuse as main transcript	n.211+20400C>T	intron_variant, non_coding_transcript_variant
SBF2	NM_001386339.1 linkuse as main transcript	c.*1515G>A	3_prime_UTR_variant	41/41
SBF2	NM_001386342.1 linkuse as main transcript	c.*1515G>A	3_prime_UTR_variant	39/39

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SBF2	ENST00000256190.13 linkuse as main transcript	c.*1515G>A		3_prime_UTR_variant	40/40	1	NM_030962.4	P3	Q86WG5-1
SBF2-AS1	ENST00000663578.1 linkuse as main transcript	n.236+20400C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.334

AC:

50785

AN:

151986

Hom.:

9164

Cov.:

show subpopulations

Gnomad AFR

AF:

0.215

Gnomad AMI

AF:

0.423

Gnomad AMR

AF:

0.319

Gnomad ASJ

AF:

0.369

Gnomad EAS

AF:

0.319

Gnomad SAS

AF:

0.203

Gnomad FIN

AF:

0.477

Gnomad MID

AF:

0.297

Gnomad NFE

AF:

0.395

Gnomad OTH

AF:

0.334

GnomAD4 exome

AF:

0.479

AC:

208

AN:

434

Hom.:

Cov.:

AF XY:

0.465

AC XY:

121

AN XY:

260

show subpopulations

Gnomad4 FIN exome

AF:

0.481

Gnomad4 NFE exome

AF:

0.500

Gnomad4 OTH exome

AF:

0.333

GnomAD4 genome

AF:

0.334

AC:

50780

AN:

152106

Hom.:

9160

Cov.:

AF XY:

0.334

AC XY:

24805

AN XY:

74360

show subpopulations

Gnomad4 AFR

AF:

0.215

Gnomad4 AMR

AF:

0.319

Gnomad4 ASJ

AF:

0.369

Gnomad4 EAS

AF:

0.319

Gnomad4 SAS

AF:

0.202

Gnomad4 FIN

AF:

0.477

Gnomad4 NFE

AF:

0.395

Gnomad4 OTH

AF:

0.329

Alfa

AF:

0.372

Hom.:

14715

Bravo

AF:

0.317

Asia WGS

AF:

0.235

AC:

819

AN:

3474

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Charcot-Marie-Tooth disease type 4B2

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.61

CADD

Benign

DANN

Benign

0.77

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over