2-230168917-A-ATTAATTT

Variant names:

• chr2-230168917-A-ATTAATTT
• rs5839361
• NM_080424.4:c.*206_*207insAAATTAA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The NM_080424.4(SP110):​c.*206_*207insAAATTAA 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 0.0012 (1 hom., cov: 0)
  • Exomes 𝑓: 0.023 (24 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.

• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0012 (178/148148) while in subpopulation SAS AF= 0.00318 (15/4712). AF 95% confidence interval is 0.00196. There are 1 homozygotes in gnomad4. There are 79 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High Homozygotes in GnomAdExome4 at 24 AR gene

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes AF: 0.00120 AC: 178 AN: 148082 Hom.: 1 Cov.: 0

Gnomad AFR AF: 0.00137

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000873

Gnomad ASJ AF: 0.000291

Gnomad EAS AF: 0.000590

Gnomad SAS AF: 0.00318

Gnomad FIN AF: 0.00127

Gnomad MID AF: 0.00325

Gnomad NFE AF: 0.00115

Gnomad OTH AF: 0.000492

GnomAD4 exome AF: 0.0228 AC: 6314 AN: 276538 Hom.: 24 Cov.: 0 AF XY: 0.0227 AC XY: 3354 AN XY: 147438

Gnomad4 AFR exome AF: 0.0151

Gnomad4 AMR exome AF: 0.0149

Gnomad4 ASJ exome AF: 0.0221

Gnomad4 EAS exome AF: 0.0125

Gnomad4 SAS exome AF: 0.0231

Gnomad4 FIN exome AF: 0.0219

Gnomad4 NFE exome AF: 0.0253

Gnomad4 OTH exome AF: 0.0226

GnomAD4 genome AF: 0.00120 AC: 178 AN: 148148 Hom.: 1 Cov.: 0 AF XY: 0.00110 AC XY: 79 AN XY: 72044

Gnomad4 AFR AF: 0.00136

Gnomad4 AMR AF: 0.000872

Gnomad4 ASJ AF: 0.000291

Gnomad4 EAS AF: 0.000592

Gnomad4 SAS AF: 0.00318

Gnomad4 FIN AF: 0.00127

Gnomad4 NFE AF: 0.00115

Gnomad4 OTH AF: 0.000488

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;