rs17079928

Variant names:

• chr13-24080089-G-A
• rs17079928
• ENST00000424834.6:c.-112+62388G>A

Variant summary

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

The ENST00000424834.6(SPATA13):​c.-112+62388G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 152,162 control chromosomes in the GnomAD database, including 6,090 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 0.28 (6090 hom., cov: 33)
• Consequence: SPATA13 ENST00000424834.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.335
• Publications: 8 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.304 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPATA13	NM_001286792.2	c.75+62388G>A		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+62388G>A		intron_variant	Intron 3 of 14	1		ENSP00000398560.2
ENSG00000273167	ENST00000382141.4	n.-112+62388G>A		intron_variant	Intron 3 of 15	5		ENSP00000371576.4

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42394 AN: 152044 Hom.: 6075 Cov.: 33

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.199

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.0967

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.279 AC: 42435 AN: 152162 Hom.: 6090 Cov.: 33 AF XY: 0.274 AC XY: 20362 AN XY: 74384

African (AFR) AF: 0.276 AC: 11443 AN: 41494

American (AMR) AF: 0.262 AC: 4004 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1193 AN: 3470

East Asian (EAS) AF: 0.0963 AC: 500 AN: 5190

South Asian (SAS) AF: 0.128 AC: 616 AN: 4826

European-Finnish (FIN) AF: 0.274 AC: 2900 AN: 10574

Middle Eastern (MID) AF: 0.238 AC: 69 AN: 290

European-Non Finnish (NFE) AF: 0.308 AC: 20916 AN: 68002

Other (OTH) AF: 0.290 AC: 613 AN: 2114

Alfa AF: 0.299 Hom.: 20146

Bravo AF: 0.279

Asia WGS AF: 0.110 AC: 385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.3
DANN	Benign	0.50
PhyloP100		0.34
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: rs17079928; hg19: chr13-24654228; COSMIC: COSV66150415;