rs587780464

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP6_Very_Strong

The NM_018013.4(SOBP):c.1382A>C(p.His461Pro) variant causes a missense change involving the alteration of a conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.00041 ( 0 hom., cov: 32)

Exomes 𝑓: 0.000041 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

SOBP
NM_018013.4 missense

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 8.80

Publications

0 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 -8 ACMG points.

BP6

Variant 6-107634226-A-C is Benign according to our data. Variant chr6-107634226-A-C is described in CliVar as Likely_benign. Clinvar id is 130357.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-107634226-A-C is described in CliVar as Likely_benign. Clinvar id is 130357.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-107634226-A-C is described in CliVar as Likely_benign. Clinvar id is 130357.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-107634226-A-C is described in CliVar as Likely_benign. Clinvar id is 130357.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-107634226-A-C is described in CliVar as Likely_benign. Clinvar id is 130357.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-107634226-A-C is described in CliVar as Likely_benign. Clinvar id is 130357.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SOBP	NM_018013.4 link	c.1382A>C	p.His461Pro	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.1382A>C	p.His461Pro	missense_variant	Exon 6 of 7	5	NM_018013.4	ENSP00000318900.5		A7XYQ1

Frequencies

GnomAD3 genomes

AF:

0.000414

AC:

AN:

123192

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000536

Gnomad AMI

AF:

0.00139

Gnomad AMR

AF:

0.000312

Gnomad ASJ

AF:

0.000332

Gnomad EAS

AF:

0.000230

Gnomad SAS

AF:

0.000813

Gnomad FIN

AF:

0.000891

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000298

Gnomad OTH

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0000414

AC:

AN:

1425152

Hom.:

Cov.:

AF XY:

0.0000395

AC XY:

AN XY:

709534

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.0000304

AC:

AN:

32842

American (AMR)

AF:

0.0000907

AC:

AN:

44100

Ashkenazi Jewish (ASJ)

AF:

0.000117

AC:

AN:

25668

East Asian (EAS)

AF:

0.0000518

AC:

AN:

38642

South Asian (SAS)

AF:

0.0000833

AC:

AN:

84080

European-Finnish (FIN)

AF:

0.000128

AC:

AN:

39190

Middle Eastern (MID)

AF:

0.000181

AC:

AN:

5536

European-Non Finnish (NFE)

AF:

0.0000310

AC:

AN:

1095958

Other (OTH)

AF:

0.0000338

AC:

AN:

59136

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.234

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000414

AC:

AN:

123246

Hom.:

Cov.:

AF XY:

0.000534

AC XY:

AN XY:

59928

show subpopulations

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.000534

AC:

AN:

31812

American (AMR)

AF:

0.000311

AC:

AN:

12852

Ashkenazi Jewish (ASJ)

AF:

0.000332

AC:

AN:

3014

East Asian (EAS)

AF:

0.000231

AC:

AN:

4330

South Asian (SAS)

AF:

0.000818

AC:

AN:

3668

European-Finnish (FIN)

AF:

0.000891

AC:

AN:

7856

Middle Eastern (MID)

AF:

0.00

AC:

AN:

242

European-Non Finnish (NFE)

AF:

0.000298

AC:

AN:

57006

Other (OTH)

AF:

0.00

AC:

AN:

1748

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.289

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<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:

0.00581

Hom.:

Asia WGS

AF:

0.00318

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Aug 07, 2013

Genetic Services Laboratory, University of Chicago

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.20

BayesDel_addAF

Uncertain

0.060

BayesDel_noAF

Benign

-0.15

CADD

Uncertain

(source)

DANN

Uncertain

0.99

DEOGEN2

Benign

0.19

Eigen

Uncertain

0.68

Eigen_PC

Pathogenic

0.67

FATHMM_MKL

Pathogenic

0.99

LIST_S2

Benign

0.80

M_CAP

Pathogenic

0.30

MetaRNN

Uncertain

0.66

MetaSVM

Benign

-1.0

MutationAssessor

Uncertain

2.1

PhyloP100

8.8

PrimateAI

Uncertain

0.65

PROVEAN

Uncertain

-2.5

REVEL

Uncertain

0.33

Sift

Uncertain

0.0030

Sift4G

Benign

0.32

Polyphen

1.0

Vest4

0.68

MutPred

0.30

Gain of glycosylation at H461 (P = 0.0129);

MVP

0.17

ClinPred

0.82

GERP RS

5.1

Varity_R

0.35

gMVP

0.47

Mutation Taster

=54/46

polymorphism

(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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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