Variant rs9486659 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_018013.4(SOBP):c.2047A>G(p.Ser683Gly) variant causes a missense change. The variant allele was found at a frequency of 0.988 in 1,312,578 control chromosomes in the GnomAD database, including 640,415 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.98 ( 71114 hom., cov: 30)

Exomes 𝑓: 0.99 ( 569301 hom. )

Consequence

SOBP
NM_018013.4 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 5.03

Variant links:

Genes affected

SOBP (HGNC:29256): (sine oculis binding protein homolog) The protein encoded by this gene is a nuclear zinc finger protein that is involved in development of the cochlea. Defects in this gene have also been linked to intellectual disability. [provided by RefSeq, Mar 2011]

SOBP 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 (MetaRNN=5.850178E-7).

BP6

Variant 6-107634891-A-G is Benign according to our data. Variant chr6-107634891-A-G is described in ClinVar as [Benign]. Clinvar id is 130361.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-107634891-A-G is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.982 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SOBP	NM_018013.4 linkuse as main transcript	c.2047A>G	p.Ser683Gly	missense_variant	6/7	ENST00000317357.10	NP_060483.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SOBP	ENST00000317357.10 linkuse as main transcript	c.2047A>G	p.Ser683Gly	missense_variant	6/7	5	NM_018013.4	ENSP00000318900	P1

Frequencies

GnomAD3 genomes

AF:

0.979

AC:

145148

AN:

148300

Hom.:

71060

Cov.:

show subpopulations

Gnomad AFR

AF:

0.955

Gnomad AMI

AF:

1.00

Gnomad AMR

AF:

0.977

Gnomad ASJ

AF:

0.973

Gnomad EAS

AF:

1.00

Gnomad SAS

AF:

0.992

Gnomad FIN

AF:

1.00

Gnomad MID

AF:

0.962

Gnomad NFE

AF:

0.989

Gnomad OTH

AF:

0.969

GnomAD3 exomes

AF:

0.988

AC:

69669

AN:

70520

Hom.:

34418

AF XY:

0.989

AC XY:

40375

AN XY:

40838

show subpopulations

Gnomad AFR exome

AF:

0.964

Gnomad AMR exome

AF:

0.989

Gnomad ASJ exome

AF:

0.972

Gnomad EAS exome

AF:

1.00

Gnomad SAS exome

AF:

0.994

Gnomad FIN exome

AF:

0.999

Gnomad NFE exome

AF:

0.987

Gnomad OTH exome

AF:

0.975

GnomAD4 exome

AF:

0.989

AC:

1151270

AN:

1164172

Hom.:

569301

Cov.:

AF XY:

0.989

AC XY:

562487

AN XY:

568742

show subpopulations

Gnomad4 AFR exome

AF:

0.956

Gnomad4 AMR exome

AF:

0.985

Gnomad4 ASJ exome

AF:

0.972

Gnomad4 EAS exome

AF:

1.00

Gnomad4 SAS exome

AF:

0.994

Gnomad4 FIN exome

AF:

0.999

Gnomad4 NFE exome

AF:

0.990

Gnomad4 OTH exome

AF:

0.984

GnomAD4 genome

AF:

0.979

AC:

145255

AN:

148406

Hom.:

71114

Cov.:

AF XY:

0.980

AC XY:

70900

AN XY:

72344

show subpopulations

Gnomad4 AFR

AF:

0.955

Gnomad4 AMR

AF:

0.977

Gnomad4 ASJ

AF:

0.973

Gnomad4 EAS

AF:

1.00

Gnomad4 SAS

AF:

0.993

Gnomad4 FIN

AF:

1.00

Gnomad4 NFE

AF:

0.989

Gnomad4 OTH

AF:

0.969

Alfa

AF:

0.984

Hom.:

8959

TwinsUK

AF:

0.989

AC:

3669

ALSPAC

AF:

0.991

AC:

3819

ExAC

AF:

0.981

AC:

19202

Asia WGS

AF:

0.992

AC:

2990

AN:

3014

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

Benign, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
Benign, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Benign, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Oct 24, 2013	- -

Intellectual disability, anterior maxillary protrusion, and strabismus

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 15, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.043

BayesDel_addAF

Benign

-0.67

BayesDel_noAF

Benign

-0.71

CADD

Benign

DANN

Benign

0.32

DEOGEN2

Benign

0.018

Eigen

Benign

-1.0

Eigen_PC

Benign

-0.89

FATHMM_MKL

Benign

0.012

LIST_S2

Benign

0.16

MetaRNN

Benign

5.9e-7

MetaSVM

Benign

-1.0

MutationAssessor

Benign

-0.34

MutationTaster

Benign

1.0

PrimateAI

Pathogenic

0.93

PROVEAN

Benign

-0.16

REVEL

Benign

0.10

Sift

Benign

0.92

Sift4G

Benign

0.45

Polyphen

0.0

Vest4

0.067

ClinPred

0.0073

GERP RS

1.9

Varity_R

0.044

gMVP

0.11

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