2-230168917-A-ATTAATT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_080424.4(SP110):c.*206_*207insAATTAA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.54 (21210 hom., cov: 0)
  • Exomes 𝑓: 0.36 (4455 hom.)
• Consequence: SP110 NM_080424.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.76

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 -10 ACMG points.

• BP6: Variant 2-230168917-A-ATTAATT is Benign according to our data. Variant chr2-230168917-A-ATTAATT is described in ClinVar as [Benign]. Clinvar id is 369333.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SP110	NM_080424.4	c.*206_*207insAATTAA		3_prime_UTR_variant	19/19	ENST00000258381.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SP110	ENST00000258381.11	c.*206_*207insAATTAA		3_prime_UTR_variant	19/19	2	NM_080424.4	P1
	ENST00000628587.2	n.1003+1267_1003+1268insAATTTT		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.536 AC: 79256 AN: 147956 Hom.: 21215 Cov.: 0

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.755

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.568

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.549

GnomAD4 exome AF: 0.358 AC: 96407 AN: 269396 Hom.: 4455 Cov.: 0 AF XY: 0.358 AC XY: 51407 AN XY: 143536

Gnomad4 AFR exome AF: 0.283

Gnomad4 AMR exome AF: 0.316

Gnomad4 ASJ exome AF: 0.379

Gnomad4 EAS exome AF: 0.265

Gnomad4 SAS exome AF: 0.344

Gnomad4 FIN exome AF: 0.363

Gnomad4 NFE exome AF: 0.378

Gnomad4 OTH exome AF: 0.367

GnomAD4 genome AF: 0.536 AC: 79282 AN: 148030 Hom.: 21210 Cov.: 0 AF XY: 0.532 AC XY: 38278 AN XY: 71974

Gnomad4 AFR AF: 0.444

Gnomad4 AMR AF: 0.515

Gnomad4 ASJ AF: 0.608

Gnomad4 EAS AF: 0.433

Gnomad4 SAS AF: 0.554

Gnomad4 FIN AF: 0.564

Gnomad4 NFE AF: 0.591

Gnomad4 OTH AF: 0.552

Alfa AF: 0.374 Hom.: 612

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Hepatic veno-occlusive disease-immunodeficiency syndrome Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5839361; hg19: chr2-231033633;