rs1553839905

Variant names:

• chr2-230168917-ATTT-A
• rs1553839905
• NM_080424.4:c.*204_*206delAAA

Your query was ambiguous. Multiple possible variants found:

• chr2-230168917-ATTT-A
• chr2-230168917-ATTT-AT
• chr2-230168917-ATTT-ATT
• chr2-230168917-ATTT-ATTTT
• chr2-230168917-ATTT-ATTTTT
• chr2-230168917-ATTT-ATTTTTT
• chr2-230168917-ATTT-ATTTTTTT
• chr2-230168917-ATTT-ATTTTTTTT
• chr2-230168917-ATTT-ATTTTTTTTT
• chr2-230168917-ATTT-ATTTTTTTTTT
• chr2-230168917-ATTT-ATTTTTTTTTTT
• chr2-230168917-ATTT-ATTTTTTTTTTTT
• chr2-230168917-ATTT-ATTTTTTTTTTTTT
• chr2-230168917-ATTT-ATTTTTTTTTTTTTT
• chr2-230168917-ATTT-ATTTTTTTTTTTTTTT
• chr2-230168917-ATTT-ATTTTTTTTTTTTTTTT
• chr2-230168917-ATTT-ATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_080424.4(SP110):​c.*204_*206delAAA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000798 in 425,864 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000027 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00011 (0 hom.)
• Consequence: SP110 NM_080424.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.114
• Publications: 0 publications found

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]

SP110 Gene-Disease associations (from GenCC):

• hepatic veno-occlusive disease-immunodeficiency syndrome

  Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), PanelApp Australia, Orphanet, ClinGen, Ambry Genetics

ENSG00000225963 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_080424.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SP110	NM_080424.4	MANE Select	c.*204_*206delAAA		3_prime_UTR	Exon 19 of 19	NP_536349.3	Q9HB58-6
	SP110	NM_001378442.1		c.*204_*206delAAA		3_prime_UTR	Exon 20 of 20	NP_001365371.1
	SP110	NM_001378443.1		c.*204_*206delAAA		3_prime_UTR	Exon 19 of 19	NP_001365372.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SP110	ENST00000258381.11	TSL:2 MANE Select	c.*204_*206delAAA		3_prime_UTR	Exon 19 of 19	ENSP00000258381.6	Q9HB58-6
	SP110	ENST00000358662.9	TSL:1	c.*204_*206delAAA		3_prime_UTR	Exon 18 of 18	ENSP00000351488.4	Q9HB58-1
	SP110	ENST00000897327.1		c.*204_*206delAAA		splice_region	Exon 19 of 19	ENSP00000567386.1

Frequencies

GnomAD3 genomes AF: 0.0000270 AC: 4 AN: 148108 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0000497

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000197

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000149

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.000108 AC: 30 AN: 277756 Hom.: 0 AF XY: 0.0000878 AC XY: 13 AN XY: 148066

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.000228 AC: 2 AN: 8766

American (AMR) AF: 0.00 AC: 0 AN: 13088

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 8300

East Asian (EAS) AF: 0.000292 AC: 6 AN: 20536

South Asian (SAS) AF: 0.0000573 AC: 2 AN: 34894

European-Finnish (FIN) AF: 0.0000674 AC: 1 AN: 14842

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1148

European-Non Finnish (NFE) AF: 0.000112 AC: 18 AN: 160584

Other (OTH) AF: 0.0000641 AC: 1 AN: 15598

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.0000270 AC: 4 AN: 148108 Hom.: 0 Cov.: 0 AF XY: 0.0000139 AC XY: 1 AN XY: 71984

African (AFR) AF: 0.0000497 AC: 2 AN: 40266

American (AMR) AF: 0.00 AC: 0 AN: 14886

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3434

East Asian (EAS) AF: 0.000197 AC: 1 AN: 5082

South Asian (SAS) AF: 0.00 AC: 0 AN: 4722

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 9450

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 308

European-Non Finnish (NFE) AF: 0.0000149 AC: 1 AN: 67026

Other (OTH) AF: 0.00 AC: 0 AN: 2036

Alfa AF: 0.00 Hom.: 25

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.11
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs1553839905; hg19: chr2-231033633;