rs9553166

Positions:

• chr13-24093562-A-G

Variant summary

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

The ENST00000424834.6(SPATA13):​c.-112+75861A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0906 in 152,230 control chromosomes in the GnomAD database, including 826 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 0.091 (826 hom., cov: 32)
• Consequence: SPATA13 ENST00000424834.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.560

Genes affected

SPATA13 (HGNC:23222): (spermatogenesis associated 13) Enables guanyl-nucleotide exchange factor activity and identical protein binding activity. Involved in cell migration; plasma membrane bounded cell projection assembly; and regulation of cell migration. Located in several cellular components, including filopodium; lamellipodium; and ruffle membrane. [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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SPATA13	NM_001286792.2	c.75+75861A>G		intron_variant			NP_001273721.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPATA13	ENST00000424834.6	c.-112+75861A>G		intron_variant		1		ENSP00000398560

Frequencies

GnomAD3 genomes AF: 0.0906 AC: 13785 AN: 152110 Hom.: 823 Cov.: 32

Gnomad AFR AF: 0.0234

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.0815

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.0906 AC: 13798 AN: 152230 Hom.: 826 Cov.: 32 AF XY: 0.0908 AC XY: 6760 AN XY: 74436

Gnomad4 AFR AF: 0.0234

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.0815

Gnomad4 NFE AF: 0.115

Gnomad4 OTH AF: 0.108

Alfa AF: 0.117 Hom.: 1152

Bravo AF: 0.0915

Asia WGS AF: 0.154 AC: 535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.58
DANN	Benign	0.37

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: rs9553166; hg19: chr13-24667701;