rs5839361

Variant names:

• chr2-230168917-A-ATTAAT
• rs5839361
• NM_080424.4:c.*206_*207insATTAA

Your query was ambiguous. Multiple possible variants found:

• chr2-230168917-A-ATTAAT
• chr2-230168917-A-ATTAATT
• chr2-230168917-A-ATTAATTT
• chr2-230168917-A-ATTAATTTT
• chr2-230168917-A-ATTAATTTTT
• chr2-230168917-A-ATTAATTTTTT
• chr2-230168917-A-ATTAATTTTTTT
• chr2-230168917-A-ATTATT
• chr2-230168917-A-ATTATTT
• chr2-230168917-A-ATTATTTT

Variant summary

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

The NM_080424.4(SP110):​c.*206_*207insATTAA 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 0.033 (196 hom., cov: 0)
  • Exomes 𝑓: 0.14 (289 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 (AFR) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SP110	NM_080424.4	c.*206_*207insATTAA		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.*206_*207insATTAA		3_prime_UTR_variant	Exon 19 of 19	2	NM_080424.4	ENSP00000258381.6

Frequencies

GnomAD3 genomes AF: 0.0328 AC: 4857 AN: 147918 Hom.: 195 Cov.: 0

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0149

Gnomad ASJ AF: 0.00233

Gnomad EAS AF: 0.00197

Gnomad SAS AF: 0.000635

Gnomad FIN AF: 0.0133

Gnomad MID AF: 0.00325

Gnomad NFE AF: 0.00373

Gnomad OTH AF: 0.0295

GnomAD4 exome AF: 0.136 AC: 37290 AN: 273532 Hom.: 289 Cov.: 0 AF XY: 0.135 AC XY: 19647 AN XY: 145830

Gnomad4 AFR exome AF: 0.170

Gnomad4 AMR exome AF: 0.108

Gnomad4 ASJ exome AF: 0.149

Gnomad4 EAS exome AF: 0.0821

Gnomad4 SAS exome AF: 0.116

Gnomad4 FIN exome AF: 0.131

Gnomad4 NFE exome AF: 0.147

Gnomad4 OTH exome AF: 0.143

GnomAD4 genome AF: 0.0330 AC: 4878 AN: 147986 Hom.: 196 Cov.: 0 AF XY: 0.0323 AC XY: 2325 AN XY: 71950

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.0148

Gnomad4 ASJ AF: 0.00233

Gnomad4 EAS AF: 0.00197

Gnomad4 SAS AF: 0.000637

Gnomad4 FIN AF: 0.0133

Gnomad4 NFE AF: 0.00373

Gnomad4 OTH AF: 0.0292

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: rs5839361; hg19: chr2-231033633;