Genetic Variant SP110:c.*197_*206dupAAAAAAAAAA (chr2-230168917-A-ATTTTTTTTTT) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_080424.4(SP110):c.*197_*206dupAAAAAAAAAA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.034 ( 124 hom., cov: 0)

Exomes 𝑓: 0.0059 ( 32 hom. )

Consequence

SP110
NM_080424.4 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.76

Publications

0 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 -8 ACMG points.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0555 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SP110	NM_080424.4 link	c.197_206dupAAAAAAAAAA		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.197_206dupAAAAAAAAAA		3_prime_UTR_variant	Exon 19 of 19	2	NM_080424.4	ENSP00000258381.6		Q9HB58-6

Frequencies

GnomAD3 genomes

AF:

0.0339

AC:

5016

AN:

147788

Hom.:

124

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00877

Gnomad AMI

AF:

0.0156

Gnomad AMR

AF:

0.0218

Gnomad ASJ

AF:

0.0181

Gnomad EAS

AF:

0.000787

Gnomad SAS

AF:

0.00636

Gnomad FIN

AF:

0.0378

Gnomad MID

AF:

0.0162

Gnomad NFE

AF:

0.0570

Gnomad OTH

AF:

0.0271

GnomAD4 exome

AF:

0.00591

AC:

1639

AN:

277296

Hom.:

Cov.:

AF XY:

0.00569

AC XY:

841

AN XY:

147794

show subpopulations

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

African (AFR)

AF:

0.00103

AC:

AN:

8762

American (AMR)

AF:

0.00283

AC:

AN:

13068

Ashkenazi Jewish (ASJ)

AF:

0.00301

AC:

AN:

8294

East Asian (EAS)

AF:

0.00

AC:

AN:

20556

South Asian (SAS)

AF:

0.00355

AC:

124

AN:

34894

European-Finnish (FIN)

AF:

0.00661

AC:

AN:

14818

Middle Eastern (MID)

AF:

0.00436

AC:

AN:

1148

European-Non Finnish (NFE)

AF:

0.00780

AC:

1249

AN:

160184

Other (OTH)

AF:

0.00591

AC:

AN:

15572

⚠️ 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: 0.382

Heterozygous variant carriers

144

216

288

360

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0339

AC:

5014

AN:

147858

Hom.:

124

Cov.:

AF XY:

0.0321

AC XY:

2308

AN XY:

71882

show subpopulations

African (AFR)

AF:

0.00875

AC:

353

AN:

40328

American (AMR)

AF:

0.0218

AC:

324

AN:

14872

Ashkenazi Jewish (ASJ)

AF:

0.0181

AC:

AN:

3428

East Asian (EAS)

AF:

0.000789

AC:

AN:

5068

South Asian (SAS)

AF:

0.00637

AC:

AN:

4710

European-Finnish (FIN)

AF:

0.0378

AC:

354

AN:

9358

Middle Eastern (MID)

AF:

0.0142

AC:

AN:

282

European-Non Finnish (NFE)

AF:

0.0570

AC:

3814

AN:

66868

Other (OTH)

AF:

0.0269

AC:

AN:

2046

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.432

Heterozygous variant carriers

207

414

622

829

1036

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0230

Hom.:

ClinVar

Not reported in ClinVar

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-ATTT-ATTTTTTTTTTTTT

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over