rs9511156

chr13-24223648-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001166271.3(SPATA13):c.719G>A(p.Arg240Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0749 in 1,552,072 control chromosomes in the GnomAD database, including 5,113 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.056 (348 hom., cov: 33)
  • Exomes 𝑓: 0.077 (4765 hom.)
• Consequence: SPATA13 NM_001166271.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.23

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 (MetaRNN=0.0017323196).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0828 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPATA13	NM_001166271.3	c.719G>A	p.Arg240Lys	missense_variant	2/13	ENST00000382108.8
SPATA13	NM_001286792.2	c.905G>A	p.Arg302Lys	missense_variant	4/15
SPATA13	NM_153023.4	c.-222-25829G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPATA13	ENST00000382108.8	c.719G>A	p.Arg240Lys	missense_variant	2/13	5	NM_001166271.3
SPATA13	ENST00000424834.6	c.719G>A	p.Arg240Lys	missense_variant	4/15	1
SPATA13	ENST00000382095.8	c.-222-25829G>A		intron_variant		2
SPATA13	ENST00000466831.2	n.1041G>A		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes AF: 0.0558 AC: 8497 AN: 152232 Hom.: 348 Cov.: 33

Gnomad AFR AF: 0.0141

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.0416

Gnomad ASJ AF: 0.0302

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0132

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0847

Gnomad OTH AF: 0.0449

GnomAD3 exomes AF: 0.0565 AC: 8927 AN: 158070 Hom.: 388 AF XY: 0.0551 AC XY: 4600 AN XY: 83452

Gnomad AFR exome AF: 0.0128

Gnomad AMR exome AF: 0.0315

Gnomad ASJ exome AF: 0.0291

Gnomad EAS exome AF: 0.0000917

Gnomad SAS exome AF: 0.0159

Gnomad FIN exome AF: 0.115

Gnomad NFE exome AF: 0.0848

Gnomad OTH exome AF: 0.0598

GnomAD4 exome AF: 0.0770 AC: 107779 AN: 1399722 Hom.: 4765 Cov.: 30 AF XY: 0.0754 AC XY: 52073 AN XY: 690356

Gnomad4 AFR exome AF: 0.0113

Gnomad4 AMR exome AF: 0.0326

Gnomad4 ASJ exome AF: 0.0299

Gnomad4 EAS exome AF: 0.0000839

Gnomad4 SAS exome AF: 0.0161

Gnomad4 FIN exome AF: 0.113

Gnomad4 NFE exome AF: 0.0881

Gnomad4 OTH exome AF: 0.0611

GnomAD4 genome AF: 0.0558 AC: 8495 AN: 152350 Hom.: 348 Cov.: 33 AF XY: 0.0543 AC XY: 4048 AN XY: 74496

Gnomad4 AFR AF: 0.0141

Gnomad4 AMR AF: 0.0416

Gnomad4 ASJ AF: 0.0302

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0133

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.0847

Gnomad4 OTH AF: 0.0445

Alfa AF: 0.0739 Hom.: 805

Bravo AF: 0.0489

TwinsUK AF: 0.0968 AC: 359

ALSPAC AF: 0.0968 AC: 373

ESP6500AA AF: 0.0152 AC: 21

ESP6500EA AF: 0.0858 AC: 273

ExAC AF: 0.0451 AC: 1174

Asia WGS AF: 0.00751 AC: 27 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.58	T
BayesDel_noAF	Benign	-0.53
Cadd	Benign	0.22
Dann	Benign	0.54
Eigen	Benign	-1.1
Eigen_PC	Benign	-1.2
FATHMM_MKL	Benign	0.022	N
MetaRNN	Benign	0.0017	T;T
MetaSVM	Benign	-1.1	T
MutationTaster	Benign	1.0	N;N
PrimateAI	Benign	0.27	T
Sift4G	Benign	1.0	T;T
Vest4		0.012
MPC		0.30
ClinPred		0.0038	T
GERP RS		-0.89
gMVP		0.061

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: rs9511156; hg19: chr13-24797786;