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GeneBe

rs957683

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_080424.4(SP110):c.1349-405A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.758 in 152,114 control chromosomes in the GnomAD database, including 44,220 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 ( 44220 hom., cov: 32)

Consequence

SP110
NM_080424.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.761
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.97).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.81 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SP110NM_080424.4 linkuse as main transcriptc.1349-405A>G intron_variant ENST00000258381.11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SP110ENST00000258381.11 linkuse as main transcriptc.1349-405A>G intron_variant 2 NM_080424.4 P1Q9HB58-6

Frequencies

GnomAD3 genomes
AF:
0.758
AC:
115140
AN:
151996
Hom.:
44184
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.730
Gnomad AMI
AF:
0.931
Gnomad AMR
AF:
0.706
Gnomad ASJ
AF:
0.858
Gnomad EAS
AF:
0.450
Gnomad SAS
AF:
0.674
Gnomad FIN
AF:
0.701
Gnomad MID
AF:
0.861
Gnomad NFE
AF:
0.815
Gnomad OTH
AF:
0.781
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.758
AC:
115233
AN:
152114
Hom.:
44220
Cov.:
32
AF XY:
0.747
AC XY:
55567
AN XY:
74352
show subpopulations
Gnomad4 AFR
AF:
0.730
Gnomad4 AMR
AF:
0.706
Gnomad4 ASJ
AF:
0.858
Gnomad4 EAS
AF:
0.451
Gnomad4 SAS
AF:
0.674
Gnomad4 FIN
AF:
0.701
Gnomad4 NFE
AF:
0.815
Gnomad4 OTH
AF:
0.782
Alfa
AF:
0.789
Hom.:
9668
Bravo
AF:
0.756
Asia WGS
AF:
0.583
AC:
2030
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
Cadd
Benign
4.0
Dann
Benign
0.77

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs957683; hg19: chr2-231043376; API