13-24084217-G-T

Variant names:

• chr13-24084217-G-T
• rs9805786
• ENST00000424834.6:c.-112+66516G>T

Variant summary

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

The ENST00000424834.6(SPATA13):​c.-112+66516G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.632 in 151,954 control chromosomes in the GnomAD database, including 30,788 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 0.63 (30788 hom., cov: 32)
• Consequence: SPATA13 ENST00000424834.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.259
• Publications: 8 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.741 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPATA13	NM_001286792.2	c.75+66516G>T		intron_variant	Intron 3 of 14		NP_001273721.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPATA13	ENST00000424834.6	c.-112+66516G>T		intron_variant	Intron 3 of 14	1		ENSP00000398560.2
ENSG00000273167	ENST00000382141.4	n.-112+66516G>T		intron_variant	Intron 3 of 15	5		ENSP00000371576.4

Frequencies

GnomAD3 genomes AF: 0.631 AC: 95874 AN: 151836 Hom.: 30733 Cov.: 32

Gnomad AFR AF: 0.747

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.636

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.586

Gnomad OTH AF: 0.621

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

GnomAD4 genome AF: 0.632 AC: 95989 AN: 151954 Hom.: 30788 Cov.: 32 AF XY: 0.632 AC XY: 46923 AN XY: 74248

African (AFR) AF: 0.748 AC: 30985 AN: 41444

American (AMR) AF: 0.596 AC: 9100 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.666 AC: 2309 AN: 3468

East Asian (EAS) AF: 0.539 AC: 2778 AN: 5158

South Asian (SAS) AF: 0.637 AC: 3065 AN: 4810

European-Finnish (FIN) AF: 0.576 AC: 6077 AN: 10546

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.586 AC: 39781 AN: 67940

Other (OTH) AF: 0.624 AC: 1316 AN: 2108

Alfa AF: 0.609 Hom.: 92973

Bravo AF: 0.638

Asia WGS AF: 0.621 AC: 2163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.60
DANN	Benign	0.74
PhyloP100		-0.26
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs9805786; hg19: chr13-24658356;