rs13018234

Variant names:

• chr2-230172150-G-A
• rs13018234
• NM_080424.4:c.1731C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-230172150-G-A
• chr2-230172150-G-C

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_Strong BP6_Very_Strong BP7 BA1

The NM_080424.4(SP110):​c.1731C>T​(p.Cys577Cys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 1,608,768 control chromosomes in the GnomAD database, including 10,935 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.10 (847 hom., cov: 33)
  • Exomes 𝑓: 0.11 (10088 hom.)
• Consequence: SP110 NM_080424.4 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:4
• Conservation: PhyloP100: 2.46

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]

ENSG00000225963 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -21 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BP6: Variant 2-230172150-G-A is Benign according to our data. Variant chr2-230172150-G-A is described in ClinVar as [Benign]. Clinvar id is 334898.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-230172150-G-A is described in Lovd as [Benign].
• BP7: Synonymous conserved (PhyloP=2.46 with no splicing effect.
• 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	c.1731C>T	p.Cys577Cys	synonymous_variant	Exon 16 of 19	ENST00000258381.11	NP_536349.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SP110	ENST00000258381.11	c.1731C>T	p.Cys577Cys	synonymous_variant	Exon 16 of 19	2	NM_080424.4	ENSP00000258381.6

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15400 AN: 152168 Hom.: 846 Cov.: 33

Gnomad AFR AF: 0.0888

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.0597

Gnomad FIN AF: 0.0861

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.101

GnomAD3 exomes AF: 0.0949 AC: 23860 AN: 251346 Hom.: 1333 AF XY: 0.0955 AC XY: 12970 AN XY: 135842

Gnomad AFR exome AF: 0.0853

Gnomad AMR exome AF: 0.0783

Gnomad ASJ exome AF: 0.0967

Gnomad EAS exome AF: 0.000490

Gnomad SAS exome AF: 0.0690

Gnomad FIN exome AF: 0.0883

Gnomad NFE exome AF: 0.125

Gnomad OTH exome AF: 0.0979

GnomAD4 exome AF: 0.113 AC: 163971 AN: 1456482 Hom.: 10088 Cov.: 30 AF XY: 0.112 AC XY: 80895 AN XY: 724922

Gnomad4 AFR exome AF: 0.0878

Gnomad4 AMR exome AF: 0.0793

Gnomad4 ASJ exome AF: 0.0959

Gnomad4 EAS exome AF: 0.000378

Gnomad4 SAS exome AF: 0.0700

Gnomad4 FIN exome AF: 0.0917

Gnomad4 NFE exome AF: 0.124

Gnomad4 OTH exome AF: 0.106

GnomAD4 genome AF: 0.101 AC: 15419 AN: 152286 Hom.: 847 Cov.: 33 AF XY: 0.0991 AC XY: 7381 AN XY: 74476

Gnomad4 AFR AF: 0.0890

Gnomad4 AMR AF: 0.101

Gnomad4 ASJ AF: 0.100

Gnomad4 EAS AF: 0.00212

Gnomad4 SAS AF: 0.0605

Gnomad4 FIN AF: 0.0861

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.101

Alfa AF: 0.103 Hom.: 627

Bravo AF: 0.102

Asia WGS AF: 0.0320 AC: 113 AN: 3478

EpiCase AF: 0.118

EpiControl AF: 0.124

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Hepatic veno-occlusive disease-immunodeficiency syndrome Benign:2

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 12, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

not specified Benign:1

Mar 29, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

not provided Benign:1

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	15
DANN	Benign	0.67

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.12		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs13018234; hg19: chr2-231036866;