rs17079773

Variant names:

• chr13-24024245-C-T
• rs17079773
• ENST00000424834.6:c.-112+6544C>T

Variant summary

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

The ENST00000424834.6(SPATA13):​c.-112+6544C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,124 control chromosomes in the GnomAD database, including 1,475 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 0.12 (1475 hom., cov: 32)
• Consequence: SPATA13 ENST00000424834.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.832
• Publications: 12 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 (EAS) allele frequency at 95% confidence interval = 0.423 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPATA13	NM_001286792.2	c.75+6544C>T		intron_variant	Intron 3 of 14		NP_001273721.1
SPATA13	NR_104595.2	n.365+6544C>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPATA13	ENST00000424834.6	c.-112+6544C>T		intron_variant	Intron 3 of 14	1		ENSP00000398560.2
ENSG00000273167	ENST00000382141.4	n.-112+6544C>T		intron_variant	Intron 3 of 15	5		ENSP00000371576.4
SPATA13	ENST00000439928.2	n.357+6544C>T		intron_variant	Intron 3 of 4	1

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17998 AN: 152006 Hom.: 1478 Cov.: 32

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.0755

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.0328

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0802

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.118 AC: 17995 AN: 152124 Hom.: 1475 Cov.: 32 AF XY: 0.120 AC XY: 8915 AN XY: 74360

African (AFR) AF: 0.147 AC: 6115 AN: 41494

American (AMR) AF: 0.155 AC: 2370 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0755 AC: 262 AN: 3470

East Asian (EAS) AF: 0.438 AC: 2262 AN: 5160

South Asian (SAS) AF: 0.177 AC: 853 AN: 4820

European-Finnish (FIN) AF: 0.0328 AC: 348 AN: 10598

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0802 AC: 5454 AN: 67994

Other (OTH) AF: 0.112 AC: 237 AN: 2112

Alfa AF: 0.0979 Hom.: 3032

Bravo AF: 0.127

Asia WGS AF: 0.277 AC: 960 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	2.3
DANN	Benign	0.56
PhyloP100		-0.83
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: rs17079773; hg19: chr13-24598384; COSMIC: COSV66150128;