NM_001166271.3:c.719G>A

Variant names:

• chr13-24223648-G-A
• rs9511156
• NM_001166271.3:c.719G>A

Variant summary

Our verdict is Benign. The variant received -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. 15/19 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
• Publications: 10 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 (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 rank	MANE	Protein	UniProt
SPATA13	NM_001166271.3	c.719G>A	p.Arg240Lys	missense_variant	Exon 2 of 13	ENST00000382108.8	NP_001159743.1
SPATA13	NM_001286792.2	c.905G>A	p.Arg302Lys	missense_variant	Exon 4 of 15		NP_001273721.1
SPATA13	NM_153023.4	c.-222-25829G>A		intron_variant	Intron 1 of 11		NP_694568.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPATA13	ENST00000382108.8	c.719G>A	p.Arg240Lys	missense_variant	Exon 2 of 13	5	NM_001166271.3	ENSP00000371542.3
ENSG00000273167	ENST00000382141.4	n.719G>A		non_coding_transcript_exon_variant	Exon 4 of 16	5		ENSP00000371576.4

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

GnomAD2 exomes AF: 0.0565 AC: 8927 AN: 158070 AF XY: 0.0551

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 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

African (AFR) AF: 0.0113 AC: 358 AN: 31600

American (AMR) AF: 0.0326 AC: 1164 AN: 35708

Ashkenazi Jewish (ASJ) AF: 0.0299 AC: 754 AN: 25182

East Asian (EAS) AF: 0.0000839 AC: 3 AN: 35740

South Asian (SAS) AF: 0.0161 AC: 1277 AN: 79236

European-Finnish (FIN) AF: 0.113 AC: 5563 AN: 49368

Middle Eastern (MID) AF: 0.00772 AC: 44 AN: 5700

European-Non Finnish (NFE) AF: 0.0881 AC: 95064 AN: 1079066

Other (OTH) AF: 0.0611 AC: 3552 AN: 58122

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

African (AFR) AF: 0.0141 AC: 586 AN: 41594

American (AMR) AF: 0.0416 AC: 636 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0302 AC: 105 AN: 3472

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5180

South Asian (SAS) AF: 0.0133 AC: 64 AN: 4828

European-Finnish (FIN) AF: 0.113 AC: 1199 AN: 10624

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0847 AC: 5760 AN: 68026

Other (OTH) AF: 0.0445 AC: 94 AN: 2114

Alfa AF: 0.0705 Hom.: 1109

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
AlphaMissense	Benign	0.086
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
LIST_S2	Benign	0.51	.;T
MetaRNN	Benign	0.0017	T;T
MetaSVM	Benign	-1.1	T
PhyloP100		1.2
PrimateAI	Benign	0.27	T
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	T
GERP RS		-0.89
gMVP		0.061
Mutation Taster		=96/4	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: rs9511156; hg19: chr13-24797786; COSMIC: COSV107482174; COSMIC: COSV107482174;