Variant rs587780464 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

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 -8 ACMG points.

BP6

Variant 6-107634226-A-C is Benign according to our data. Variant chr6-107634226-A-C is described in ClinVar 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/exons	MANE	Protein	UniProt
SOBP	NM_018013.4 linkuse as main transcript	c.1382A>C	p.His461Pro	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.1382A>C	p.His461Pro	missense_variant	6/7	5	NM_018013.4	ENSP00000318900	P1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

123192

Hom.:

Cov.:

FAILED QC

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

Gnomad4 AFR exome

AF:

0.0000304

Gnomad4 AMR exome

AF:

0.0000907

Gnomad4 ASJ exome

AF:

0.000117

Gnomad4 EAS exome

AF:

0.0000518

Gnomad4 SAS exome

AF:

0.0000833

Gnomad4 FIN exome

AF:

0.000128

Gnomad4 NFE exome

AF:

0.0000310

Gnomad4 OTH exome

AF:

0.0000338

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

Gnomad4 AFR

AF:

0.000534

Gnomad4 AMR

AF:

0.000311

Gnomad4 ASJ

AF:

0.000332

Gnomad4 EAS

AF:

0.000231

Gnomad4 SAS

AF:

0.000818

Gnomad4 FIN

AF:

0.000891

Gnomad4 NFE

AF:

0.000298

Gnomad4 OTH

AF:

0.00

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

Likely benign, criteria provided, single submitter

clinical testing

Genetic Services Laboratory, University of Chicago

Aug 07, 2013

- -

not provided

Benign:1

Likely benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

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

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

MutationTaster

Benign

1.0

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

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