chr2-230179651-T-C

Position:

• chr2-230179651-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.1349-1396A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.434 in 151,564 control chromosomes in the GnomAD database, including 14,824 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 0.43 (14824 hom., cov: 29)
• Consequence: SP110 NM_080424.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SP110	NM_080424.4	c.1349-1396A>G		intron_variant		ENST00000258381.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SP110	ENST00000258381.11	c.1349-1396A>G		intron_variant		2	NM_080424.4	P1

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65758 AN: 151446 Hom.: 14795 Cov.: 29

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.434 AC: 65819 AN: 151564 Hom.: 14824 Cov.: 29 AF XY: 0.428 AC XY: 31726 AN XY: 74046

Gnomad4 AFR AF: 0.517

Gnomad4 AMR AF: 0.319

Gnomad4 ASJ AF: 0.473

Gnomad4 EAS AF: 0.128

Gnomad4 SAS AF: 0.370

Gnomad4 FIN AF: 0.415

Gnomad4 NFE AF: 0.439

Gnomad4 OTH AF: 0.414

Alfa AF: 0.428 Hom.: 13846

Bravo AF: 0.430

Asia WGS AF: 0.280 AC: 974 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.0
DANN	Benign	0.65

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: rs11678451; hg19: chr2-231044367;