Variant 6-107635075-A-AGCC details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 1P and 16B. PM4_SupportingBP6_Very_StrongBS1BS2

The NM_018013.4(SOBP):c.2250_2252dupGCC(p.Pro751dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00118 in 1,564,964 control chromosomes in the GnomAD database, including 7 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0052 ( 3 hom., cov: 31)

Exomes 𝑓: 0.00075 ( 4 hom. )

Consequence

SOBP
NM_018013.4 disruptive_inframe_insertion

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.353

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:

SOBP (HGNC:):

SOBP links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

PM4

Nonframeshift variant in NON repetitive region in NM_018013.4. Strenght limited to Supporting due to length of the change: 1aa.

BP6

Variant 6-107635075-A-AGCC is Benign according to our data. Variant chr6-107635075-A-AGCC is described in ClinVar as [Benign]. Clinvar id is 716871.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00524 (784/149698) while in subpopulation AFR AF= 0.0175 (718/41012). AF 95% confidence interval is 0.0164. There are 3 homozygotes in gnomad4. There are 369 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SOBP	NM_018013.4 linkuse as main transcript	c.2250_2252dupGCC	p.Pro751dup	disruptive_inframe_insertion	6/7	ENST00000317357.10	NP_060483.3	A7XYQ1Q24K27

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SOBP	ENST00000317357.10 linkuse as main transcript	c.2250_2252dupGCC	p.Pro751dup	disruptive_inframe_insertion	6/7	5	NM_018013.4	ENSP00000318900.5		A7XYQ1
SOBP	ENST00000494935.1 linkuse as main transcript	n.105_107dupGCC		non_coding_transcript_exon_variant	1/2	3

Frequencies

GnomAD3 genomes

AF:

0.00523

AC:

782

AN:

149596

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0175

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00172

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000396

Gnomad SAS

AF:

0.000209

Gnomad FIN

AF:

0.000201

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000417

Gnomad OTH

AF:

0.00339

GnomAD3 exomes

AF:

0.00174

AC:

235

AN:

135090

Hom.:

AF XY:

0.00131

AC XY:

AN XY:

74636

show subpopulations

Gnomad AFR exome

AF:

0.0237

Gnomad AMR exome

AF:

0.00161

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.000452

Gnomad SAS exome

AF:

0.000295

Gnomad FIN exome

AF:

0.000203

Gnomad NFE exome

AF:

0.000610

Gnomad OTH exome

AF:

0.00168

GnomAD4 exome

AF:

0.000750

AC:

1061

AN:

1415266

Hom.:

Cov.:

AF XY:

0.000708

AC XY:

496

AN XY:

700450

show subpopulations

Gnomad4 AFR exome

AF:

0.0162

Gnomad4 AMR exome

AF:

0.00140

Gnomad4 ASJ exome

AF:

0.000119

Gnomad4 EAS exome

AF:

0.000871

Gnomad4 SAS exome

AF:

0.000319

Gnomad4 FIN exome

AF:

0.000165

Gnomad4 NFE exome

AF:

0.000298

Gnomad4 OTH exome

AF:

0.00137

GnomAD4 genome

AF:

0.00524

AC:

784

AN:

149698

Hom.:

Cov.:

AF XY:

0.00505

AC XY:

369

AN XY:

73042

show subpopulations

Gnomad4 AFR

AF:

0.0175

Gnomad4 AMR

AF:

0.00172

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000397

Gnomad4 SAS

AF:

0.000210

Gnomad4 FIN

AF:

0.000201

Gnomad4 NFE

AF:

0.000417

Gnomad4 OTH

AF:

0.00336

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genetic Services Laboratory, University of Chicago

Jun 07, 2019

- -

SOBP-related disorder

Benign:1

Likely benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 01, 2019

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over