1-9353587-C-T

Variant summary

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

The NM_025106.4(SPSB1):c.-149-2156C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 152,052 control chromosomes in the GnomAD database, including 5,475 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 0.25 (5475 hom., cov: 31)
• Consequence: SPSB1 NM_025106.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.191

Genes affected

SPSB1 (HGNC:30628): (splA/ryanodine receptor domain and SOCS box containing 1) Enables ubiquitin ligase-substrate adaptor activity. Involved in protein ubiquitination and ubiquitin-dependent protein catabolic process. Located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPSB1	NM_025106.4	c.-149-2156C>T		intron_variant		ENST00000328089.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPSB1	ENST00000328089.11	c.-149-2156C>T		intron_variant		1	NM_025106.4	P1
SPSB1	ENST00000357898.3	c.-150+1977C>T		intron_variant		5		P1
SPSB1	ENST00000450402.1	c.-149-2156C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37286 AN: 151934 Hom.: 5472 Cov.: 31

Gnomad AFR AF: 0.0938

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.245 AC: 37290 AN: 152052 Hom.: 5475 Cov.: 31 AF XY: 0.243 AC XY: 18081 AN XY: 74316

Gnomad4 AFR AF: 0.0936

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.275

Gnomad4 EAS AF: 0.285

Gnomad4 SAS AF: 0.203

Gnomad4 FIN AF: 0.341

Gnomad4 NFE AF: 0.331

Gnomad4 OTH AF: 0.255

Alfa AF: 0.310 Hom.: 10112

Bravo AF: 0.234

Asia WGS AF: 0.215 AC: 747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	8.0
Dann	Benign	0.76

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: rs11121384; hg19: chr1-9413646; COSMIC: COSV60162514; COSMIC: COSV60162514;