6-107634891-A-G

Variant names:

Variant summary

Our verdict is Benign. The variant received -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. 13/21 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

Publications

15 publications found

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 Gene-Disease associations (from GenCC):

intellectual disability, anterior maxillary protrusion, and strabismus
Inheritance: Unknown, AR Classification: SUPPORTIVE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), G2P, Orphanet
syndromic intellectual disability
Inheritance: AR Classification: LIMITED Submitted by: ClinGen

SOBP links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 CliVar 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 CliVar 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 CliVar 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 CliVar 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 CliVar 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 CliVar as Benign. Clinvar id is 130361.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SOBP	NM_018013.4 link	c.2047A>G	p.Ser683Gly	missense_variant	Exon 6 of 7	ENST00000317357.10	NP_060483.3	A7XYQ1Q24K27

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SOBP	ENST00000317357.10 link	c.2047A>G	p.Ser683Gly	missense_variant	Exon 6 of 7	5	NM_018013.4	ENSP00000318900.5		A7XYQ1
SOBP	ENST00000494935.1 link	n.-99A>G		upstream_gene_variant		3

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

GnomAD2 exomes

AF:

0.988

AC:

69669

AN:

70520

AF XY:

0.989

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 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

African (AFR)

AF:

0.956

AC:

22868

AN:

23926

American (AMR)

AF:

0.985

AC:

21548

AN:

21874

Ashkenazi Jewish (ASJ)

AF:

0.972

AC:

17919

AN:

18426

East Asian (EAS)

AF:

1.00

AC:

22153

AN:

22154

South Asian (SAS)

AF:

0.994

AC:

50032

AN:

50340

European-Finnish (FIN)

AF:

0.999

AC:

24266

AN:

24292

Middle Eastern (MID)

AF:

0.949

AC:

3106

AN:

3274

European-Non Finnish (NFE)

AF:

0.990

AC:

944916

AN:

954714

Other (OTH)

AF:

0.984

AC:

44462

AN:

45172

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.485

Heterozygous variant carriers

685

1371

2056

2742

3427

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

20798

41596

62394

83192

103990

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.979

AC:

145255

AN:

148406

Hom.:

71114

Cov.:

AF XY:

0.980

AC XY:

70900

AN XY:

72344

show subpopulations

African (AFR)

AF:

0.955

AC:

39266

AN:

41104

American (AMR)

AF:

0.977

AC:

14585

AN:

14926

Ashkenazi Jewish (ASJ)

AF:

0.973

AC:

3334

AN:

3426

East Asian (EAS)

AF:

1.00

AC:

5029

AN:

5030

South Asian (SAS)

AF:

0.993

AC:

4792

AN:

4826

European-Finnish (FIN)

AF:

1.00

AC:

9138

AN:

9142

Middle Eastern (MID)

AF:

0.955

AC:

279

AN:

292

European-Non Finnish (NFE)

AF:

0.989

AC:

65912

AN:

66676

Other (OTH)

AF:

0.969

AC:

2008

AN:

2072

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

158

316

474

632

790

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

888

1776

2664

3552

4440

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

- -

Oct 24, 2013

Genetic Services Laboratory, University of Chicago

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

- -

Intellectual disability, anterior maxillary protrusion, and strabismus

Benign:1

Jul 15, 2021

Genome-Nilou Lab

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

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

(source)

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

PhyloP100

5.0

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

Mutation Taster

=98/2

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over