rs17080058

Variant names:

• chr13-24110181-A-G
• rs17080058
• ENST00000424834.6:c.-112+92480A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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]

SPATA13 Gene-Disease associations (from GenCC):

• primary angle-closure glaucoma

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen

ENSG00000273167 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SPATA13	NM_001286792.2	c.75+92480A>G		intron_variant	Intron 3 of 14		NP_001273721.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPATA13	ENST00000424834.6	c.-112+92480A>G		intron_variant	Intron 3 of 14	1		ENSP00000398560.2
ENSG00000273167	ENST00000382141.4	n.-112+92480A>G		intron_variant	Intron 3 of 15	5		ENSP00000371576.4

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

African (AFR) AF: 0.173 AC: 7109 AN: 41140

American (AMR) AF: 0.0630 AC: 957 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.0562 AC: 195 AN: 3472

East Asian (EAS) AF: 0.000581 AC: 3 AN: 5166

South Asian (SAS) AF: 0.0618 AC: 295 AN: 4770

European-Finnish (FIN) AF: 0.119 AC: 1256 AN: 10514

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0944 AC: 6404 AN: 67812

Other (OTH) AF: 0.0921 AC: 193 AN: 2096

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
PhyloP100		-1.5
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs17080058; hg19: chr13-24684320;