2-230168917-ATTT-ATTTTTTTTTTTTT

Variant names:

• chr2-230168917-A-ATTTTTTTTTT
• rs1553839905
• NM_080424.4:c.*197_*206dupAAAAAAAAAA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_080424.4(SP110):​c.*197_*206dupAAAAAAAAAA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.034 (124 hom., cov: 0)
  • Exomes 𝑓: 0.0059 (32 hom.)
• Consequence: SP110 NM_080424.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• 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]

ENSG00000225963 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0555 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SP110	NM_080424.4	c.*197_*206dupAAAAAAAAAA		3_prime_UTR_variant	Exon 19 of 19	ENST00000258381.11	NP_536349.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SP110	ENST00000258381	c.*197_*206dupAAAAAAAAAA		3_prime_UTR_variant	Exon 19 of 19	2	NM_080424.4	ENSP00000258381.6

Frequencies

GnomAD3 genomes AF: 0.0339 AC: 5016 AN: 147788 Hom.: 124 Cov.: 0

Gnomad AFR AF: 0.00877

Gnomad AMI AF: 0.0156

Gnomad AMR AF: 0.0218

Gnomad ASJ AF: 0.0181

Gnomad EAS AF: 0.000787

Gnomad SAS AF: 0.00636

Gnomad FIN AF: 0.0378

Gnomad MID AF: 0.0162

Gnomad NFE AF: 0.0570

Gnomad OTH AF: 0.0271

GnomAD4 exome AF: 0.00591 AC: 1639 AN: 277296 Hom.: 32 Cov.: 0 AF XY: 0.00569 AC XY: 841 AN XY: 147794

Gnomad4 AFR exome AF: 0.00103

Gnomad4 AMR exome AF: 0.00283

Gnomad4 ASJ exome AF: 0.00301

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00355

Gnomad4 FIN exome AF: 0.00661

Gnomad4 NFE exome AF: 0.00780

Gnomad4 OTH exome AF: 0.00591

GnomAD4 genome AF: 0.0339 AC: 5014 AN: 147858 Hom.: 124 Cov.: 0 AF XY: 0.0321 AC XY: 2308 AN XY: 71882

Gnomad4 AFR AF: 0.00875

Gnomad4 AMR AF: 0.0218

Gnomad4 ASJ AF: 0.0181

Gnomad4 EAS AF: 0.000789

Gnomad4 SAS AF: 0.00637

Gnomad4 FIN AF: 0.0378

Gnomad4 NFE AF: 0.0570

Gnomad4 OTH AF: 0.0269

ClinVar

Not reported in ClinVar

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: rs1553839905; hg19: chr2-231033633;