rs5839361

Variant names:

• chr2-230168917-A-ATTAATT
• rs5839361
• NM_080424.4:c.*206_*207insAATTAA

Your query was ambiguous. Multiple possible variants found:

• chr2-230168917-A-ATTAATT
• chr2-230168917-A-ATTAAT
• 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. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_080424.4(SP110):​c.*206_*207insAATTAA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.54 (21210 hom., cov: 0)
  • Exomes 𝑓: 0.36 (4455 hom.)
• Consequence: SP110 NM_080424.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.76
• Publications: 1 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: Benign. The variant received -10 ACMG points.

• BP6: Variant 2-230168917-A-ATTAATT is Benign according to our data. Variant chr2-230168917-A-ATTAATT is described in ClinVar as Benign. ClinVar VariationId is 369333.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

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.*206_*207insAATTAA		3_prime_UTR	Exon 19 of 19	NP_536349.3	Q9HB58-6
	SP110	NM_001378442.1		c.*206_*207insAATTAA		3_prime_UTR	Exon 20 of 20	NP_001365371.1
	SP110	NM_001378443.1		c.*206_*207insAATTAA		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.*206_*207insAATTAA		3_prime_UTR	Exon 19 of 19	ENSP00000258381.6	Q9HB58-6
	SP110	ENST00000358662.9	TSL:1	c.*206_*207insAATTAA		3_prime_UTR	Exon 18 of 18	ENSP00000351488.4	Q9HB58-1
	SP110	ENST00000897327.1		c.*206_*207insAATTAA		splice_region	Exon 19 of 19	ENSP00000567386.1

Frequencies

GnomAD3 genomes AF: 0.536 AC: 79256 AN: 147956 Hom.: 21215 Cov.: 0

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.755

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.568

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.549

GnomAD4 exome AF: 0.358 AC: 96407 AN: 269396 Hom.: 4455 Cov.: 0 AF XY: 0.358 AC XY: 51407 AN XY: 143536

African (AFR) AF: 0.283 AC: 2401 AN: 8488

American (AMR) AF: 0.316 AC: 3933 AN: 12446

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 3075 AN: 8118

East Asian (EAS) AF: 0.265 AC: 5283 AN: 19924

South Asian (SAS) AF: 0.344 AC: 11544 AN: 33558

European-Finnish (FIN) AF: 0.363 AC: 5262 AN: 14506

Middle Eastern (MID) AF: 0.364 AC: 405 AN: 1112

European-Non Finnish (NFE) AF: 0.378 AC: 58936 AN: 156054

Other (OTH) AF: 0.367 AC: 5568 AN: 15190

GnomAD4 genome AF: 0.536 AC: 79282 AN: 148030 Hom.: 21210 Cov.: 0 AF XY: 0.532 AC XY: 38278 AN XY: 71974

African (AFR) AF: 0.444 AC: 17884 AN: 40294

American (AMR) AF: 0.515 AC: 7654 AN: 14872

Ashkenazi Jewish (ASJ) AF: 0.608 AC: 2089 AN: 3436

East Asian (EAS) AF: 0.433 AC: 2188 AN: 5056

South Asian (SAS) AF: 0.554 AC: 2607 AN: 4708

European-Finnish (FIN) AF: 0.564 AC: 5328 AN: 9444

Middle Eastern (MID) AF: 0.574 AC: 162 AN: 282

European-Non Finnish (NFE) AF: 0.591 AC: 39560 AN: 66990

Other (OTH) AF: 0.552 AC: 1132 AN: 2050

Alfa AF: 0.374 Hom.: 612

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	Hepatic veno-occlusive disease-immunodeficiency syndrome (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-1.8

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs5839361; hg19: chr2-231033633;