rs13018234

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_080424.4(SP110):c.1731C>T(p.Cys577Cys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 1,608,768 control chromosomes in the GnomAD database, including 10,935 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.10 ( 847 hom., cov: 33)

Exomes 𝑓: 0.11 ( 10088 hom. )

Consequence

SP110
NM_080424.4 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 2.46

Publications

14 publications found

Variant links:

Genes affected

SP110 (HGNC:5401): (SP110 nuclear body protein) The nuclear body is a multiprotein complex that may have a role in the regulation of gene transcription. This gene is a member of the SP100/SP140 family of nuclear body proteins and encodes a leukocyte-specific nuclear body component. The protein can function as an activator of gene transcription and may serve as a nuclear hormone receptor coactivator. In addition, it has been suggested that the protein may play a role in ribosome biogenesis and in the induction of myeloid cell differentiation. Alternative splicing has been observed for this gene and three transcript variants, encoding distinct isoforms, have been identified. [provided by RefSeq, Jul 2008]

SP110 Gene-Disease associations (from GenCC):

hepatic veno-occlusive disease-immunodeficiency syndrome
Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, ClinGen, Ambry Genetics

SP110 links:

ENSG00000225963 (HGNC:):

ENSG00000225963 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.64).

BP6

Variant 2-230172150-G-A is Benign according to our data. Variant chr2-230172150-G-A is described in ClinVar as [Benign]. Clinvar id is 334898.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=2.46 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SP110	NM_080424.4 link	c.1731C>T	p.Cys577Cys	synonymous_variant	Exon 16 of 19	ENST00000258381.11	NP_536349.3	Q9HB58-6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SP110	ENST00000258381.11 link	c.1731C>T	p.Cys577Cys	synonymous_variant	Exon 16 of 19	2	NM_080424.4	ENSP00000258381.6		Q9HB58-6

Frequencies

GnomAD3 genomes

AF:

0.101

AC:

15400

AN:

152168

Hom.:

846

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0888

Gnomad AMI

AF:

0.103

Gnomad AMR

AF:

0.101

Gnomad ASJ

AF:

0.100

Gnomad EAS

AF:

0.00212

Gnomad SAS

AF:

0.0597

Gnomad FIN

AF:

0.0861

Gnomad MID

AF:

0.137

Gnomad NFE

AF:

0.121

Gnomad OTH

AF:

0.101

GnomAD2 exomes

AF:

0.0949

AC:

23860

AN:

251346

AF XY:

0.0955

show subpopulations

Gnomad AFR exome

AF:

0.0853

Gnomad AMR exome

AF:

0.0783

Gnomad ASJ exome

AF:

0.0967

Gnomad EAS exome

AF:

0.000490

Gnomad FIN exome

AF:

0.0883

Gnomad NFE exome

AF:

0.125

Gnomad OTH exome

AF:

0.0979

GnomAD4 exome

AF:

0.113

AC:

163971

AN:

1456482

Hom.:

10088

Cov.:

AF XY:

0.112

AC XY:

80895

AN XY:

724922

show subpopulations

African (AFR)

AF:

0.0878

AC:

2929

AN:

33364

American (AMR)

AF:

0.0793

AC:

3548

AN:

44720

Ashkenazi Jewish (ASJ)

AF:

0.0959

AC:

2506

AN:

26118

East Asian (EAS)

AF:

0.000378

AC:

AN:

39682

South Asian (SAS)

AF:

0.0700

AC:

6031

AN:

86210

European-Finnish (FIN)

AF:

0.0917

AC:

4897

AN:

53388

Middle Eastern (MID)

AF:

0.114

AC:

659

AN:

5760

European-Non Finnish (NFE)

AF:

0.124

AC:

136977

AN:

1107000

Other (OTH)

AF:

0.106

AC:

6409

AN:

60240

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.452

Heterozygous variant carriers

6863

13726

20590

27453

34316

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.101

AC:

15419

AN:

152286

Hom.:

847

Cov.:

AF XY:

0.0991

AC XY:

7381

AN XY:

74476

show subpopulations

African (AFR)

AF:

0.0890

AC:

3696

AN:

41544

American (AMR)

AF:

0.101

AC:

1548

AN:

15310

Ashkenazi Jewish (ASJ)

AF:

0.100

AC:

347

AN:

3468

East Asian (EAS)

AF:

0.00212

AC:

AN:

5184

South Asian (SAS)

AF:

0.0605

AC:

292

AN:

4824

European-Finnish (FIN)

AF:

0.0861

AC:

914

AN:

10618

Middle Eastern (MID)

AF:

0.140

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.121

AC:

8263

AN:

68022

Other (OTH)

AF:

0.101

AC:

213

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

708

1415

2123

2830

3538

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.104

Hom.:

881

Bravo

AF:

0.102

Asia WGS

AF:

0.0320

AC:

113

AN:

3478

EpiCase

AF:

0.118

EpiControl

AF:

0.124

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Hepatic veno-occlusive disease-immunodeficiency syndrome

Benign:2

Jan 12, 2018

Illumina Laboratory Services, Illumina

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not specified

Benign:1

Mar 29, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.64

CADD

Benign

(source)

DANN

Benign

0.67

PhyloP100

2.5

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.12

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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rs13018234

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