2-230168917-ATTT-ATTTTTTTTTTTT

Variant names:

• chr2-230168917-A-ATTTTTTTTT
• rs1553839905
• NM_080424.4:c.*198_*206dupAAAAAAAAA

Variant summary

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

The NM_080424.4(SP110):​c.*198_*206dupAAAAAAAAA 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 0.042 (193 hom., cov: 0)
  • Exomes 𝑓: 0.011 (63 hom.)
  • Failed GnomAD Quality Control
• 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 nfe. gnomad4_exome allele frequency = 0.0111 (3074/276862) while in subpopulation NFE AF= 0.0132 (2110/159976). AF 95% confidence interval is 0.0127. There are 63 homozygotes in gnomad4_exome. There are 1634 alleles in male gnomad4_exome subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High Homozygotes in GnomAdExome4 at 63 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SP110	NM_080424.4	c.*198_*206dupAAAAAAAAA		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.*198_*206dupAAAAAAAAA		3_prime_UTR_variant	Exon 19 of 19	2	NM_080424.4	ENSP00000258381.6

Frequencies

GnomAD3 genomes AF: 0.00 AC: 6144 AN: 147826 Hom.: 193 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.0164

Gnomad AMI AF: 0.0857

Gnomad AMR AF: 0.0624

Gnomad ASJ AF: 0.0755

Gnomad EAS AF: 0.00118

Gnomad SAS AF: 0.0443

Gnomad FIN AF: 0.0188

Gnomad MID AF: 0.0909

Gnomad NFE AF: 0.0551

Gnomad OTH AF: 0.0577

GnomAD4 exome AF: 0.0111 AC: 3074 AN: 276862 Hom.: 63 Cov.: 0 AF XY: 0.0111 AC XY: 1634 AN XY: 147570

Gnomad4 AFR exome AF: 0.00229

Gnomad4 AMR exome AF: 0.0116

Gnomad4 ASJ exome AF: 0.0104

Gnomad4 EAS exome AF: 0.0000486

Gnomad4 SAS exome AF: 0.0112

Gnomad4 FIN exome AF: 0.00953

Gnomad4 NFE exome AF: 0.0132

Gnomad4 OTH exome AF: 0.0103

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0415 AC: 6144 AN: 147896 Hom.: 193 Cov.: 0 AF XY: 0.0405 AC XY: 2909 AN XY: 71900

Gnomad4 AFR AF: 0.0164

Gnomad4 AMR AF: 0.0623

Gnomad4 ASJ AF: 0.0755

Gnomad4 EAS AF: 0.00118

Gnomad4 SAS AF: 0.0449

Gnomad4 FIN AF: 0.0188

Gnomad4 NFE AF: 0.0551

Gnomad4 OTH AF: 0.0572

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;