dbSNP rs1004869: SP110:c.1591-1596G>T (chr2-230174555-C-A) – 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.1591-1596G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 151,884 control chromosomes in the GnomAD database, including 990 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 0.11 ( 990 hom., cov: 32)

Consequence

SP110
NM_080424.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00

Publications

4 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:

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=-1.0).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SP110	NM_080424.4 link	c.1591-1596G>T		intron_variant	Intron 14 of 18	ENST00000258381.11	NP_536349.3	Q9HB58-6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
SP110	ENST00000258381.11 link	c.1591-1596G>T	intron_variant	Intron 14 of 18	2	NM_080424.4	ENSP00000258381.6	Q9HB58-6
SP110	ENST00000358662.9 link	c.1591-1596G>T	intron_variant	Intron 14 of 17	1		ENSP00000351488.4	Q9HB58-1
SP110	ENST00000698099.1 link	n.1591-1596G>T	intron_variant	Intron 14 of 18			ENSP00000513563.1	Q9HB58-1
SP110	ENST00000698100.1 link	n.1441-1596G>T	intron_variant	Intron 13 of 16			ENSP00000513564.1	A0A8V8TN67

Frequencies

GnomAD3 genomes

AF:

0.111

AC:

16819

AN:

151766

Hom.:

989

Cov.:

show subpopulations

Gnomad AFR

AF:

0.124

Gnomad AMI

AF:

0.103

Gnomad AMR

AF:

0.104

Gnomad ASJ

AF:

0.102

Gnomad EAS

AF:

0.00231

Gnomad SAS

AF:

0.0619

Gnomad FIN

AF:

0.0836

Gnomad MID

AF:

0.136

Gnomad NFE

AF:

0.121

Gnomad OTH

AF:

0.109

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.111

AC:

16841

AN:

151884

Hom.:

990

Cov.:

AF XY:

0.109

AC XY:

8073

AN XY:

74250

show subpopulations

African (AFR)

AF:

0.124

AC:

5145

AN:

41392

American (AMR)

AF:

0.104

AC:

1591

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.102

AC:

354

AN:

3472

East Asian (EAS)

AF:

0.00232

AC:

AN:

5180

South Asian (SAS)

AF:

0.0628

AC:

303

AN:

4824

European-Finnish (FIN)

AF:

0.0836

AC:

881

AN:

10534

Middle Eastern (MID)

AF:

0.139

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.121

AC:

8191

AN:

67894

Other (OTH)

AF:

0.108

AC:

229

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.468

Heterozygous variant carriers

666

1332

1997

2663

3329

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

188

376

564

752

940

<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:

0.118

Hom.:

699

Bravo

AF:

0.114

Asia WGS

AF:

0.0370

AC:

130

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.51

(source)

DANN

Benign

0.22

PhyloP100

0.0

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over