dbSNP rs13010639: SP110:c.1888-268G>A (chr2-230171029-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_080424.4(SP110):c.1888-268G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 539,118 control chromosomes in the GnomAD database, including 3,101 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.093 ( 746 hom., cov: 32)

Exomes 𝑓: 0.10 ( 2355 hom. )

Consequence

SP110
NM_080424.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.141

Publications

13 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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

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.1888-268G>A		intron_variant	Intron 17 of 18	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.1888-268G>A		intron_variant	Intron 17 of 18	2	NM_080424.4	ENSP00000258381.6		Q9HB58-6

Frequencies

GnomAD3 genomes

AF:

0.0931

AC:

14174

AN:

152172

Hom.:

746

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0605

Gnomad AMI

AF:

0.101

Gnomad AMR

AF:

0.0983

Gnomad ASJ

AF:

0.0999

Gnomad EAS

AF:

0.00212

Gnomad SAS

AF:

0.0598

Gnomad FIN

AF:

0.0865

Gnomad MID

AF:

0.136

Gnomad NFE

AF:

0.121

Gnomad OTH

AF:

0.0984

GnomAD4 exome

AF:

0.103

AC:

39916

AN:

386828

Hom.:

2355

AF XY:

0.101

AC XY:

20738

AN XY:

204504

show subpopulations

African (AFR)

AF:

0.0642

AC:

722

AN:

11238

American (AMR)

AF:

0.0899

AC:

1521

AN:

16926

Ashkenazi Jewish (ASJ)

AF:

0.0965

AC:

1145

AN:

11862

East Asian (EAS)

AF:

0.000158

AC:

AN:

25252

South Asian (SAS)

AF:

0.0701

AC:

3010

AN:

42930

European-Finnish (FIN)

AF:

0.0979

AC:

2192

AN:

22386

Middle Eastern (MID)

AF:

0.114

AC:

192

AN:

1678

European-Non Finnish (NFE)

AF:

0.124

AC:

28807

AN:

232228

Other (OTH)

AF:

0.104

AC:

2323

AN:

22328

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1711

3423

5134

6846

8557

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

126

252

378

504

630

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0932

AC:

14187

AN:

152290

Hom.:

746

Cov.:

AF XY:

0.0915

AC XY:

6814

AN XY:

74468

show subpopulations

African (AFR)

AF:

0.0605

AC:

2516

AN:

41554

American (AMR)

AF:

0.0982

AC:

1503

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.0999

AC:

347

AN:

3472

East Asian (EAS)

AF:

0.00212

AC:

AN:

5186

South Asian (SAS)

AF:

0.0608

AC:

294

AN:

4832

European-Finnish (FIN)

AF:

0.0865

AC:

917

AN:

10606

Middle Eastern (MID)

AF:

0.139

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.121

AC:

8259

AN:

68016

Other (OTH)

AF:

0.0978

AC:

207

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

685

1370

2055

2740

3425

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

160

320

480

640

800

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0992

Hom.:

567

Bravo

AF:

0.0922

Asia WGS

AF:

0.0310

AC:

107

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

6.9

(source)

DANN

Benign

0.76

PhyloP100

0.14

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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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