rs17080058

Positions:

• chr13-24110181-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+92480A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 151,364 control chromosomes in the GnomAD database, including 1,051 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 0.11 (1051 hom., cov: 29)
• Consequence: SPATA13 ENST00000424834.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPATA13	NM_001286792.2	c.75+92480A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPATA13	ENST00000424834.6	c.-112+92480A>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16489 AN: 151246 Hom.: 1050 Cov.: 29

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.0695

Gnomad AMR AF: 0.0631

Gnomad ASJ AF: 0.0562

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.0622

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0945

Gnomad OTH AF: 0.0935

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

GnomAD4 genome AF: 0.109 AC: 16495 AN: 151364 Hom.: 1051 Cov.: 29 AF XY: 0.108 AC XY: 7949 AN XY: 73922

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.0630

Gnomad4 ASJ AF: 0.0562

Gnomad4 EAS AF: 0.000581

Gnomad4 SAS AF: 0.0618

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.0944

Gnomad4 OTH AF: 0.0921

Alfa AF: 0.0968 Hom.: 178

Bravo AF: 0.107

Asia WGS AF: 0.0370 AC: 129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.014
DANN	Benign	0.25

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs17080058; hg19: chr13-24684320;