rs722555

chr2-230168800-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.*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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20

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=-0.88).
• 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/exons	MANE	UniProt
SP110	NM_080424.4	c.*324G>A		3_prime_UTR_variant	19/19	ENST00000258381.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SP110	ENST00000258381.11	c.*324G>A		3_prime_UTR_variant	19/19	2	NM_080424.4	P1
	ENST00000628587.2	n.1003+1148C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.570 AC: 86433 AN: 151696 Hom.: 24717 Cov.: 31

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.: 0 AF XY: 0.530 AC XY: 28569 AN XY: 53860

Gnomad4 AFR exome AF: 0.491

Gnomad4 AMR exome AF: 0.469

Gnomad4 ASJ exome AF: 0.542

Gnomad4 EAS exome AF: 0.388

Gnomad4 SAS exome AF: 0.496

Gnomad4 FIN exome AF: 0.523

Gnomad4 NFE exome AF: 0.564

Gnomad4 OTH exome AF: 0.542

GnomAD4 genome AF: 0.570 AC: 86505 AN: 151814 Hom.: 24738 Cov.: 31 AF XY: 0.565 AC XY: 41910 AN XY: 74158

Gnomad4 AFR AF: 0.551

Gnomad4 AMR AF: 0.528

Gnomad4 ASJ AF: 0.612

Gnomad4 EAS AF: 0.433

Gnomad4 SAS AF: 0.551

Gnomad4 FIN AF: 0.580

Gnomad4 NFE AF: 0.596

Gnomad4 OTH AF: 0.583

Alfa AF: 0.590 Hom.: 25819

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
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs722555; hg19: chr2-231033516;