2-230194717-T-C

Position:

• chr2-230194717-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_080424.4(SP110):​c.1129+6168A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.764 in 152,178 control chromosomes in the GnomAD database, including 44,518 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.76 (44518 hom., cov: 32)
• Consequence: SP110 NM_080424.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0550

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]

SP140 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SP110	NM_080424.4	c.1129+6168A>G		intron_variant		ENST00000258381.11	NP_536349.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SP110	ENST00000258381.11	c.1129+6168A>G		intron_variant		2	NM_080424.4	ENSP00000258381	P1

Frequencies

GnomAD3 genomes AF: 0.764 AC: 116169 AN: 152060 Hom.: 44493 Cov.: 32

Gnomad AFR AF: 0.724

Gnomad AMI AF: 0.798

Gnomad AMR AF: 0.826

Gnomad ASJ AF: 0.737

Gnomad EAS AF: 0.816

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.803

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.772

Gnomad OTH AF: 0.762

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.764 AC: 116240 AN: 152178 Hom.: 44518 Cov.: 32 AF XY: 0.765 AC XY: 56899 AN XY: 74378

Gnomad4 AFR AF: 0.723

Gnomad4 AMR AF: 0.826

Gnomad4 ASJ AF: 0.737

Gnomad4 EAS AF: 0.816

Gnomad4 SAS AF: 0.677

Gnomad4 FIN AF: 0.803

Gnomad4 NFE AF: 0.772

Gnomad4 OTH AF: 0.762

Alfa AF: 0.756 Hom.: 5451

Bravo AF: 0.766

Asia WGS AF: 0.748 AC: 2601 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	12
DANN	Benign	0.75

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs930031; hg19: chr2-231059433;