Variant rs3814700 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001424318.1(SBF2):c.-3+185A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0716 in 152,252 control chromosomes in the GnomAD database, including 607 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 0.072 ( 606 hom., cov: 33)

Exomes 𝑓: 0.066 ( 1 hom. )

Consequence

SBF2
NM_001424318.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.837

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:

ADM-DT (HGNC:55516): (ADM divergent transcript)

ADM-DT links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.7).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Protein
SBF2	NM_001424318.1 link	c.-3+185A>G	intron_variant	NP_001411247.1
SBF2	NM_001425070.1 link	c.-3+1389A>G	intron_variant	NP_001411999.1
SBF2	NM_001425069.1 link	c.-3+1389A>G	intron_variant	NP_001411998.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADM-DT	ENST00000526906.1 link	n.410-61A>G		intron_variant		2
SBF2	ENST00000685217.1 link	n.386+1381A>G		intron_variant

Frequencies

GnomAD3 genomes

AF:

0.0716

AC:

10884

AN:

151906

Hom.:

603

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0265

Gnomad AMI

AF:

0.0747

Gnomad AMR

AF:

0.118

Gnomad ASJ

AF:

0.0510

Gnomad EAS

AF:

0.279

Gnomad SAS

AF:

0.0542

Gnomad FIN

AF:

0.0563

Gnomad MID

AF:

0.0605

Gnomad NFE

AF:

0.0775

Gnomad OTH

AF:

0.0805

GnomAD4 exome

AF:

0.0658

AC:

AN:

228

Hom.:

Cov.:

AF XY:

0.0592

AC XY:

AN XY:

152

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.118

Gnomad4 NFE exome

AF:

0.0595

Gnomad4 OTH exome

AF:

0.0500

GnomAD4 genome

AF:

0.0716

AC:

10889

AN:

152024

Hom.:

606

Cov.:

AF XY:

0.0720

AC XY:

5352

AN XY:

74310

show subpopulations

Gnomad4 AFR

AF:

0.0264

Gnomad4 AMR

AF:

0.118

Gnomad4 ASJ

AF:

0.0510

Gnomad4 EAS

AF:

0.280

Gnomad4 SAS

AF:

0.0542

Gnomad4 FIN

AF:

0.0563

Gnomad4 NFE

AF:

0.0775

Gnomad4 OTH

AF:

0.0787

Alfa

AF:

0.0809

Hom.:

204

Bravo

AF:

0.0756

Asia WGS

AF:

0.142

AC:

492

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

DANN

Benign

0.81

Splicing

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over