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. The variant received -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
• 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), Orphanet, ClinGen, Ambry Genetics

ENSG00000225963 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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	ENST00000258381.11	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

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

African (AFR) AF: 0.170 AC: 1468 AN: 8644

American (AMR) AF: 0.108 AC: 1390 AN: 12864

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 1220 AN: 8194

East Asian (EAS) AF: 0.0821 AC: 1668 AN: 20318

South Asian (SAS) AF: 0.116 AC: 3967 AN: 34318

European-Finnish (FIN) AF: 0.131 AC: 1926 AN: 14682

Middle Eastern (MID) AF: 0.159 AC: 179 AN: 1124

European-Non Finnish (NFE) AF: 0.147 AC: 23278 AN: 158028

Other (OTH) AF: 0.143 AC: 2194 AN: 15360

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

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

African (AFR) AF: 0.104 AC: 4201 AN: 40330

American (AMR) AF: 0.0148 AC: 220 AN: 14894

Ashkenazi Jewish (ASJ) AF: 0.00233 AC: 8 AN: 3428

East Asian (EAS) AF: 0.00197 AC: 10 AN: 5066

South Asian (SAS) AF: 0.000637 AC: 3 AN: 4712

European-Finnish (FIN) AF: 0.0133 AC: 125 AN: 9376

Middle Eastern (MID) AF: 0.00355 AC: 1 AN: 282

European-Non Finnish (NFE) AF: 0.00373 AC: 250 AN: 66948

Other (OTH) AF: 0.0292 AC: 60 AN: 2052

Alfa AF: 0.00 Hom.: 612

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs5839361; hg19: chr2-231033633;