rs10170310

Variant names:

• chr2-138521352-G-A
• rs10170310
• NM_001001664.3:c.-61+19233G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-138521352-G-A
• chr2-138521352-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001001664.3(SPOPL):​c.-61+19233G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.786 in 150,650 control chromosomes in the GnomAD database, including 46,982 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 0.79 (46982 hom., cov: 28)
• Consequence: SPOPL NM_001001664.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.841
• Publications: 15 publications found

Genes affected

SPOPL (HGNC:27934): (speckle type BTB/POZ protein like) Predicted to enable ubiquitin protein ligase binding activity. Involved in negative regulation of protein ubiquitination and proteasome-mediated ubiquitin-dependent protein catabolic process. Part of Cul3-RING ubiquitin ligase complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001001664.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPOPL	NM_001001664.3	MANE Select	c.-61+19233G>A		intron	N/A	NP_001001664.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPOPL	ENST00000280098.9	TSL:1 MANE Select	c.-61+19233G>A		intron	N/A	ENSP00000280098.4
	SPOPL	ENST00000430968.5	TSL:5	n.-61+19233G>A		intron	N/A	ENSP00000410201.1
	SPOPL	ENST00000449869.2	TSL:3	n.-61+19233G>A		intron	N/A	ENSP00000520629.1

Frequencies

GnomAD3 genomes AF: 0.786 AC: 118391 AN: 150558 Hom.: 46948 Cov.: 28

Gnomad AFR AF: 0.675

Gnomad AMI AF: 0.782

Gnomad AMR AF: 0.834

Gnomad ASJ AF: 0.794

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.864

Gnomad MID AF: 0.857

Gnomad NFE AF: 0.835

Gnomad OTH AF: 0.813

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

GnomAD4 genome AF: 0.786 AC: 118471 AN: 150650 Hom.: 46982 Cov.: 28 AF XY: 0.787 AC XY: 57884 AN XY: 73562

African (AFR) AF: 0.675 AC: 27606 AN: 40894

American (AMR) AF: 0.834 AC: 12662 AN: 15174

Ashkenazi Jewish (ASJ) AF: 0.794 AC: 2751 AN: 3466

East Asian (EAS) AF: 0.741 AC: 3776 AN: 5094

South Asian (SAS) AF: 0.765 AC: 3645 AN: 4766

European-Finnish (FIN) AF: 0.864 AC: 8822 AN: 10210

Middle Eastern (MID) AF: 0.856 AC: 250 AN: 292

European-Non Finnish (NFE) AF: 0.835 AC: 56551 AN: 67762

Other (OTH) AF: 0.815 AC: 1696 AN: 2082

Alfa AF: 0.814 Hom.: 205418

Bravo AF: 0.776

Asia WGS AF: 0.761 AC: 2643 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.34
DANN	Benign	0.70
PhyloP100		-0.84
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10170310; hg19: chr2-139278922;