dbSNP rs722555: SP110:c.*324G>A (chr2-230168800-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.*324G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 252,654 control chromosomes in the GnomAD database, including 39,484 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 0.57 ( 24738 hom., cov: 31)

Exomes 𝑓: 0.53 ( 14746 hom. )

Consequence

SP110
NM_080424.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.20

Publications

12 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:

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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=-0.88).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SP110	NM_080424.4 link	c.*324G>A		3_prime_UTR_variant	Exon 19 of 19	ENST00000258381.11	NP_536349.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SP110	ENST00000258381.11 link	c.*324G>A		3_prime_UTR_variant	Exon 19 of 19	2	NM_080424.4	ENSP00000258381.6

Frequencies

GnomAD3 genomes

AF:

0.570

AC:

86433

AN:

151696

Hom.:

24717

Cov.:

show subpopulations

Gnomad AFR

AF:

0.551

Gnomad AMI

AF:

0.757

Gnomad AMR

AF:

0.528

Gnomad ASJ

AF:

0.612

Gnomad EAS

AF:

0.433

Gnomad SAS

AF:

0.552

Gnomad FIN

AF:

0.580

Gnomad MID

AF:

0.579

Gnomad NFE

AF:

0.596

Gnomad OTH

AF:

0.580

GnomAD4 exome

AF:

0.533

AC:

53751

AN:

100840

Hom.:

14746

Cov.:

AF XY:

0.530

AC XY:

28569

AN XY:

53860

show subpopulations

African (AFR)

AF:

0.491

AC:

1566

AN:

3188

American (AMR)

AF:

0.469

AC:

2273

AN:

4844

Ashkenazi Jewish (ASJ)

AF:

0.542

AC:

1500

AN:

2766

East Asian (EAS)

AF:

0.388

AC:

2428

AN:

6260

South Asian (SAS)

AF:

0.496

AC:

7191

AN:

14506

European-Finnish (FIN)

AF:

0.523

AC:

2126

AN:

4066

Middle Eastern (MID)

AF:

0.561

AC:

222

AN:

396

European-Non Finnish (NFE)

AF:

0.564

AC:

33523

AN:

59422

Other (OTH)

AF:

0.542

AC:

2922

AN:

5392

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.480

Heterozygous variant carriers

1093

2186

3278

4371

5464

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

268

536

804

1072

1340

<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:

0.570

AC:

86505

AN:

151814

Hom.:

24738

Cov.:

AF XY:

0.565

AC XY:

41910

AN XY:

74158

show subpopulations

African (AFR)

AF:

0.551

AC:

22802

AN:

41374

American (AMR)

AF:

0.528

AC:

8044

AN:

15246

Ashkenazi Jewish (ASJ)

AF:

0.612

AC:

2123

AN:

3470

East Asian (EAS)

AF:

0.433

AC:

2242

AN:

5172

South Asian (SAS)

AF:

0.551

AC:

2655

AN:

4816

European-Finnish (FIN)

AF:

0.580

AC:

6081

AN:

10488

Middle Eastern (MID)

AF:

0.585

AC:

172

AN:

294

European-Non Finnish (NFE)

AF:

0.596

AC:

40472

AN:

67942

Other (OTH)

AF:

0.583

AC:

1225

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1893

3786

5679

7572

9465

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

742

1484

2226

2968

3710

<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:

0.587

Hom.:

33385

Bravo

AF:

0.564

Asia WGS

AF:

0.513

AC:

1787

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

8.3

(source)

DANN

Benign

0.43

PhyloP100

1.2

Splicing

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