13-24265299-A-G

Variant names:

• chr13-24265299-A-G
• rs17464589
• NM_001166271.3:c.2164+13437A>G

Variant summary

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

The NM_001166271.3(SPATA13):​c.2164+13437A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 152,052 control chromosomes in the GnomAD database, including 9,708 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 0.35 (9708 hom., cov: 32)
• Consequence: SPATA13 NM_001166271.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.111
• Publications: 4 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.399 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001166271.3. 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
	SPATA13	NM_001166271.3	MANE Select	c.2164+13437A>G		intron	N/A	NP_001159743.1
	SPATA13	NM_001286792.2		c.2350+13437A>G		intron	N/A	NP_001273721.1
	SPATA13	NM_153023.4		c.289+13437A>G		intron	N/A	NP_694568.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATA13	ENST00000382108.8	TSL:5 MANE Select	c.2164+13437A>G		intron	N/A	ENSP00000371542.3
	SPATA13	ENST00000424834.6	TSL:1	c.2164+13437A>G		intron	N/A	ENSP00000398560.2
	ENSG00000273167	ENST00000382141.4	TSL:5	n.1798+13437A>G		intron	N/A	ENSP00000371576.4

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52861 AN: 151934 Hom.: 9703 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.0811

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.410

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.348 AC: 52895 AN: 152052 Hom.: 9708 Cov.: 32 AF XY: 0.342 AC XY: 25405 AN XY: 74306

African (AFR) AF: 0.304 AC: 12614 AN: 41488

American (AMR) AF: 0.284 AC: 4341 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1389 AN: 3468

East Asian (EAS) AF: 0.0803 AC: 415 AN: 5168

South Asian (SAS) AF: 0.316 AC: 1521 AN: 4808

European-Finnish (FIN) AF: 0.377 AC: 3979 AN: 10550

Middle Eastern (MID) AF: 0.428 AC: 124 AN: 290

European-Non Finnish (NFE) AF: 0.403 AC: 27359 AN: 67972

Other (OTH) AF: 0.359 AC: 759 AN: 2112

Alfa AF: 0.384 Hom.: 15225

Bravo AF: 0.340

Asia WGS AF: 0.260 AC: 907 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.18
PhyloP100		-0.11
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: rs17464589; hg19: chr13-24839437;