Genetic Variant SP110:c.*206_*207insAATTAA (chr2-230168917-A-ATTAATT) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_080424.4(SP110):c.*206_*207insAATTAA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.54 ( 21210 hom., cov: 0)

Exomes 𝑓: 0.36 ( 4455 hom. )

Consequence

SP110
NM_080424.4 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.76

Publications

1 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 -10 ACMG points.

BP6

Variant 2-230168917-A-ATTAATT is Benign according to our data. Variant chr2-230168917-A-ATTAATT is described in ClinVar as [Benign]. Clinvar id is 369333.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SP110	NM_080424.4 link	c.206_207insAATTAA		3_prime_UTR_variant	Exon 19 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.206_207insAATTAA		3_prime_UTR_variant	Exon 19 of 19	2	NM_080424.4	ENSP00000258381.6		Q9HB58-6

Frequencies

GnomAD3 genomes

AF:

0.536

AC:

79256

AN:

147956

Hom.:

21215

Cov.:

show subpopulations

Gnomad AFR

AF:

0.444

Gnomad AMI

AF:

0.755

Gnomad AMR

AF:

0.515

Gnomad ASJ

AF:

0.608

Gnomad EAS

AF:

0.432

Gnomad SAS

AF:

0.554

Gnomad FIN

AF:

0.564

Gnomad MID

AF:

0.568

Gnomad NFE

AF:

0.591

Gnomad OTH

AF:

0.549

GnomAD4 exome

AF:

0.358

AC:

96407

AN:

269396

Hom.:

4455

Cov.:

AF XY:

0.358

AC XY:

51407

AN XY:

143536

show subpopulations

African (AFR)

AF:

0.283

AC:

2401

AN:

8488

American (AMR)

AF:

0.316

AC:

3933

AN:

12446

Ashkenazi Jewish (ASJ)

AF:

0.379

AC:

3075

AN:

8118

East Asian (EAS)

AF:

0.265

AC:

5283

AN:

19924

South Asian (SAS)

AF:

0.344

AC:

11544

AN:

33558

European-Finnish (FIN)

AF:

0.363

AC:

5262

AN:

14506

Middle Eastern (MID)

AF:

0.364

AC:

405

AN:

1112

European-Non Finnish (NFE)

AF:

0.378

AC:

58936

AN:

156054

Other (OTH)

AF:

0.367

AC:

5568

AN:

15190

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.464

Heterozygous variant carriers

2704

5407

8111

10814

13518

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.536

AC:

79282

AN:

148030

Hom.:

21210

Cov.:

AF XY:

0.532

AC XY:

38278

AN XY:

71974

show subpopulations

African (AFR)

AF:

0.444

AC:

17884

AN:

40294

American (AMR)

AF:

0.515

AC:

7654

AN:

14872

Ashkenazi Jewish (ASJ)

AF:

0.608

AC:

2089

AN:

3436

East Asian (EAS)

AF:

0.433

AC:

2188

AN:

5056

South Asian (SAS)

AF:

0.554

AC:

2607

AN:

4708

European-Finnish (FIN)

AF:

0.564

AC:

5328

AN:

9444

Middle Eastern (MID)

AF:

0.574

AC:

162

AN:

282

European-Non Finnish (NFE)

AF:

0.591

AC:

39560

AN:

66990

Other (OTH)

AF:

0.552

AC:

1132

AN:

2050

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.518

Heterozygous variant carriers

1700

3400

5099

6799

8499

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.374

Hom.:

612

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Hepatic veno-occlusive disease-immunodeficiency syndrome

Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

-1.8

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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2-230168917-A-ATTAATT

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