Variant chr11-9779274-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1

The NM_030962.4(SBF2):c.*1144A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0459 in 152,750 control chromosomes in the GnomAD database, including 501 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.046 ( 501 hom., cov: 32)

Exomes 𝑓: 0.021 ( 0 hom. )

Consequence

SBF2
NM_030962.4 3_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: 2.50

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 -18 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.25).

BP6

Variant 11-9779274-T-C is Benign according to our data. Variant chr11-9779274-T-C is described in ClinVar as [Benign]. Clinvar id is 306559.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein
SBF2	NM_030962.4 linkuse as main transcript	c.*1144A>G	3_prime_UTR_variant	40/40	ENST00000256190.13	NP_112224.1
SBF2-AS1	NR_036485.1 linkuse as main transcript	n.211+20771T>C	intron_variant, non_coding_transcript_variant
SBF2	NM_001386339.1 linkuse as main transcript	c.*1144A>G	3_prime_UTR_variant	41/41		NP_001373268.1
SBF2	NM_001386342.1 linkuse as main transcript	c.*1144A>G	3_prime_UTR_variant	39/39		NP_001373271.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SBF2	ENST00000256190.13 linkuse as main transcript	c.*1144A>G		3_prime_UTR_variant	40/40	1	NM_030962.4	ENSP00000256190	P3	Q86WG5-1
SBF2-AS1	ENST00000663578.1 linkuse as main transcript	n.236+20771T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.0459

AC:

6990

AN:

152200

Hom.:

502

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0863

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0722

Gnomad ASJ

AF:

0.000576

Gnomad EAS

AF:

0.316

Gnomad SAS

AF:

0.0128

Gnomad FIN

AF:

0.0133

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.00532

Gnomad OTH

AF:

0.0464

GnomAD4 exome

AF:

0.0209

AC:

AN:

430

Hom.:

Cov.:

AF XY:

0.0308

AC XY:

AN XY:

260

show subpopulations

Gnomad4 FIN exome

AF:

0.0212

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.0459

AC:

6997

AN:

152320

Hom.:

501

Cov.:

AF XY:

0.0470

AC XY:

3504

AN XY:

74488

show subpopulations

Gnomad4 AFR

AF:

0.0862

Gnomad4 AMR

AF:

0.0725

Gnomad4 ASJ

AF:

0.000576

Gnomad4 EAS

AF:

0.316

Gnomad4 SAS

AF:

0.0124

Gnomad4 FIN

AF:

0.0133

Gnomad4 NFE

AF:

0.00532

Gnomad4 OTH

AF:

0.0449

Alfa

AF:

0.0209

Hom.:

Bravo

AF:

0.0545

Asia WGS

AF:

0.135

AC:

468

AN:

3478

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

-0.25

CADD

Benign

DANN

Benign

0.87

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