rs13010639

Positions:

• chr2-230171029-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.141

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
SP110	NM_080424.4	c.1888-268G>A		intron_variant		ENST00000258381.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SP110	ENST00000258381.11	c.1888-268G>A		intron_variant		2	NM_080424.4	P1
	ENST00000628587.2	n.1004-1070C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0931 AC: 14174 AN: 152172 Hom.: 746 Cov.: 32

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

Gnomad4 AFR exome AF: 0.0642

Gnomad4 AMR exome AF: 0.0899

Gnomad4 ASJ exome AF: 0.0965

Gnomad4 EAS exome AF: 0.000158

Gnomad4 SAS exome AF: 0.0701

Gnomad4 FIN exome AF: 0.0979

Gnomad4 NFE exome AF: 0.124

Gnomad4 OTH exome AF: 0.104

GnomAD4 genome AF: 0.0932 AC: 14187 AN: 152290 Hom.: 746 Cov.: 32 AF XY: 0.0915 AC XY: 6814 AN XY: 74468

Gnomad4 AFR AF: 0.0605

Gnomad4 AMR AF: 0.0982

Gnomad4 ASJ AF: 0.0999

Gnomad4 EAS AF: 0.00212

Gnomad4 SAS AF: 0.0608

Gnomad4 FIN AF: 0.0865

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.0978

Alfa AF: 0.108 Hom.: 335

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
DANN	Benign	0.76

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

LitVar

Other links and lift over

dbSNP: rs13010639; hg19: chr2-231035745;