Variant rs9511156 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.23

Variant links:

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

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	Protein
SPATA13	NM_001166271.3 linkuse as main transcript	c.719G>A	p.Arg240Lys	missense_variant	2/13	ENST00000382108.8	NP_001159743.1
SPATA13	NM_001286792.2 linkuse as main transcript	c.905G>A	p.Arg302Lys	missense_variant	4/15		NP_001273721.1
SPATA13	NM_153023.4 linkuse as main transcript	c.-222-25829G>A		intron_variant			NP_694568.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
SPATA13	ENST00000382108.8 linkuse as main transcript	c.719G>A	p.Arg240Lys	missense_variant	2/13	5	NM_001166271.3	ENSP00000371542	Q96N96-6
SPATA13	ENST00000424834.6 linkuse as main transcript	c.719G>A	p.Arg240Lys	missense_variant	4/15	1		ENSP00000398560	Q96N96-6
SPATA13	ENST00000382095.8 linkuse as main transcript	c.-222-25829G>A		intron_variant		2		ENSP00000371527	Q96N96-1
SPATA13	ENST00000466831.2 linkuse as main transcript	n.1041G>A		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes

AF:

0.0558

AC:

8497

AN:

152232

Hom.:

348

Cov.:

show subpopulations

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

show subpopulations

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.:

AF XY:

0.0754

AC XY:

52073

AN XY:

690356

show subpopulations

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.:

AF XY:

0.0543

AC XY:

4048

AN XY:

74496

show subpopulations

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:

ESP6500EA

AF:

0.0858

AC:

273

ExAC

AF:

0.0451

AC:

1174

Asia WGS

AF:

0.00751

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.58

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

LIST_S2

Benign

0.51

.;T

MetaRNN

Benign

0.0017

T;T

MetaSVM

Benign

-1.1

MutationTaster

Benign

1.0

N;N

PrimateAI

Benign

0.27

PROVEAN

Benign

0.17

.;N

REVEL

Benign

0.059

Sift

Benign

1.0

.;T

Sift4G

Benign

1.0

T;T

Vest4

0.012

MPC

0.30

ClinPred

0.0038

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over