13-24185549-G-A

Variant names:

• chr13-24185549-G-A
• rs2793483
• NM_001166271.3:c.-112+24617G>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.-112+24617G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.642 in 152,026 control chromosomes in the GnomAD database, including 31,373 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 0.64 (31373 hom., cov: 32)
• Consequence: SPATA13 NM_001166271.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.11
• Publications: 2 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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.65 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001166271.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATA13	NM_001166271.3	MANE Select	c.-112+24617G>A		intron	N/A	NP_001159743.1
	SPATA13	NM_001286792.2		c.76-37270G>A		intron	N/A	NP_001273721.1
	SPATA13	NM_153023.4		c.-223+24617G>A		intron	N/A	NP_694568.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATA13	ENST00000382108.8	TSL:5 MANE Select	c.-112+24617G>A		intron	N/A	ENSP00000371542.3
	SPATA13	ENST00000424834.6	TSL:1	c.-111-37270G>A		intron	N/A	ENSP00000398560.2
	ENSG00000273167	ENST00000382141.4	TSL:5	n.-111-37270G>A		intron	N/A	ENSP00000371576.4

Frequencies

GnomAD3 genomes AF: 0.642 AC: 97469 AN: 151908 Hom.: 31338 Cov.: 32

Gnomad AFR AF: 0.651

Gnomad AMI AF: 0.716

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.655

Gnomad OTH AF: 0.642

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

GnomAD4 genome AF: 0.642 AC: 97547 AN: 152026 Hom.: 31373 Cov.: 32 AF XY: 0.639 AC XY: 47463 AN XY: 74312

African (AFR) AF: 0.651 AC: 26999 AN: 41450

American (AMR) AF: 0.543 AC: 8298 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.662 AC: 2294 AN: 3466

East Asian (EAS) AF: 0.580 AC: 2999 AN: 5168

South Asian (SAS) AF: 0.651 AC: 3137 AN: 4818

European-Finnish (FIN) AF: 0.670 AC: 7070 AN: 10558

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.655 AC: 44556 AN: 67982

Other (OTH) AF: 0.645 AC: 1358 AN: 2106

Alfa AF: 0.647 Hom.: 27606

Bravo AF: 0.630

Asia WGS AF: 0.657 AC: 2282 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.0020
DANN	Benign	0.49
PhyloP100		-2.1
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: rs2793483; hg19: chr13-24759688;