rs17464589

Positions:

• chr13-24265299-A-G

Variant summary

Our verdict is Benign. Variant got -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

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.399 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPATA13	NM_001166271.3	c.2164+13437A>G		intron_variant		ENST00000382108.8
SPATA13	NM_001286792.2	c.2350+13437A>G		intron_variant
SPATA13	NM_153023.4	c.289+13437A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPATA13	ENST00000382108.8	c.2164+13437A>G		intron_variant		5	NM_001166271.3

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

Gnomad4 AFR AF: 0.304

Gnomad4 AMR AF: 0.284

Gnomad4 ASJ AF: 0.401

Gnomad4 EAS AF: 0.0803

Gnomad4 SAS AF: 0.316

Gnomad4 FIN AF: 0.377

Gnomad4 NFE AF: 0.403

Gnomad4 OTH AF: 0.359

Alfa AF: 0.389 Hom.: 11926

Bravo AF: 0.340

Asia WGS AF: 0.260 AC: 907 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.18

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

Publications

LitVar

Other links and lift over

dbSNP: rs17464589; hg19: chr13-24839437;