rs1129411

Variant names:

• chr2-230213010-A-C
• rs1129411
• NM_080424.4:c.334T>G

Your query was ambiguous. Multiple possible variants found:

• chr2-230213010-A-C
• chr2-230213010-A-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001378442.1(SP110):​c.352T>G​(p.Trp118Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. W118R) has been classified as Benign.

• Frequency: Genomes: not found (cov: 30)
• Consequence: SP110 NM_001378442.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.189
• Publications: 33 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]

SP140 (HGNC:17133): (SP140 nuclear body protein) This gene encodes a member of the SP100 family of proteins, which are share common domains including an N-terminal homogeneously staining region domain followed by a SP100/autoimmune regulator/NucP41/P75/deformed epidermal autoregulatory factor domain, a plant homeobox zinc finger, and a bromodomain. The encoded protein is interferon-inducible and is expressed at high levels in the nuclei of leukocytes. Variants of this gene have been associated with multiple sclerosis, Crohn's disease, and chronic lymphocytic leukemia. Alternative splicing results in multiple variants. [provided by RefSeq, Aug 2016]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.05444339).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001378442.1. 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.334T>G	p.Trp112Gly	missense	Exon 4 of 19	NP_536349.3
	SP110	NM_001378442.1		c.352T>G	p.Trp118Gly	missense	Exon 5 of 20	NP_001365371.1
	SP110	NM_001378443.1		c.334T>G	p.Trp112Gly	missense	Exon 4 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.334T>G	p.Trp112Gly	missense	Exon 4 of 19	ENSP00000258381.6
	SP110	ENST00000358662.9	TSL:1	c.334T>G	p.Trp112Gly	missense	Exon 4 of 18	ENSP00000351488.4
	SP110	ENST00000258382.10	TSL:1	c.334T>G	p.Trp112Gly	missense	Exon 4 of 15	ENSP00000258382.5

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Cov.: 55

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.051
BayesDel_addAF	Benign	-0.21	T
BayesDel_noAF	Benign	-0.55
CADD	Benign	1.7
DANN	Benign	0.48
DEOGEN2	Benign	0.0010	T
Eigen	Benign	-1.9
Eigen_PC	Benign	-1.8
FATHMM_MKL	Benign	0.0044	N
LIST_S2	Benign	0.10	T
M_CAP	Benign	0.0024	T
MetaRNN	Benign	0.054	T
MetaSVM	Benign	-0.96	T
MutationAssessor	Benign	-0.97	N
PhyloP100		-0.19
PrimateAI	Benign	0.21	T
PROVEAN	Benign	1.9	N
REVEL	Benign	0.25
Sift	Benign	0.36	T
Sift4G	Benign	0.37	T
Polyphen		0.0	B
Vest4		0.15
MutPred		0.63		Gain of disorder (P = 0.0036)
MVP		0.13
MPC		0.25
ClinPred		0.063	T
GERP RS		-0.86
Varity_R		0.041
gMVP		0.19
Mutation Taster		=300/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.10		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1129411; hg19: chr2-231077725;