rs9511117

Variant names:

• chr13-24187906-A-C
• rs9511117
• NM_001166271.3:c.-112+26974A>C

Variant summary

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

The NM_001166271.3(SPATA13):​c.-112+26974A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.734 in 152,132 control chromosomes in the GnomAD database, including 45,622 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 0.73 (45622 hom., cov: 32)
• Consequence: SPATA13 NM_001166271.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.564
• Publications: 1 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=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.903 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPATA13	NM_001166271.3	c.-112+26974A>C		intron_variant	Intron 1 of 12	ENST00000382108.8	NP_001159743.1
SPATA13	NM_001286792.2	c.76-34913A>C		intron_variant	Intron 3 of 14		NP_001273721.1
SPATA13	NM_153023.4	c.-223+26974A>C		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.-112+26974A>C		intron_variant	Intron 1 of 12	5	NM_001166271.3	ENSP00000371542.3
ENSG00000273167	ENST00000382141.4	n.-111-34913A>C		intron_variant	Intron 3 of 15	5		ENSP00000371576.4

Frequencies

GnomAD3 genomes AF: 0.734 AC: 111643 AN: 152014 Hom.: 45617 Cov.: 32

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.918

Gnomad AMR AF: 0.826

Gnomad ASJ AF: 0.868

Gnomad EAS AF: 0.704

Gnomad SAS AF: 0.776

Gnomad FIN AF: 0.923

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.909

Gnomad OTH AF: 0.782

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

GnomAD4 genome AF: 0.734 AC: 111673 AN: 152132 Hom.: 45622 Cov.: 32 AF XY: 0.736 AC XY: 54743 AN XY: 74394

African (AFR) AF: 0.346 AC: 14334 AN: 41462

American (AMR) AF: 0.825 AC: 12610 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.868 AC: 3009 AN: 3468

East Asian (EAS) AF: 0.704 AC: 3644 AN: 5174

South Asian (SAS) AF: 0.776 AC: 3736 AN: 4816

European-Finnish (FIN) AF: 0.923 AC: 9786 AN: 10606

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.909 AC: 61813 AN: 68014

Other (OTH) AF: 0.784 AC: 1651 AN: 2106

Alfa AF: 0.810 Hom.: 7203

Bravo AF: 0.709

Asia WGS AF: 0.741 AC: 2578 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.34
PhyloP100		-0.56
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: rs9511117; hg19: chr13-24762045;