13-24221351-G-A

Variant names:

• chr13-24221351-G-A
• rs715921
• NM_001166271.3:c.-111-1468G>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.-111-1468G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 152,074 control chromosomes in the GnomAD database, including 6,530 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 0.28 (6530 hom., cov: 32)
• Consequence: SPATA13 NM_001166271.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.103
• Publications: 7 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: MODERATE, LIMITED Submitted by: ClinGen, PanelApp Australia

ENSG00000273167 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.486 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATA13	NM_001166271.3	MANE Select	c.-111-1468G>A		intron	N/A	NP_001159743.1	Q96N96-6
	SPATA13	NM_001286792.2		c.76-1468G>A		intron	N/A	NP_001273721.1
	SPATA13	NM_153023.4		c.-222-28126G>A		intron	N/A	NP_694568.1	Q96N96-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATA13	ENST00000382108.8	TSL:5 MANE Select	c.-111-1468G>A		intron	N/A	ENSP00000371542.3	Q96N96-6
	SPATA13	ENST00000424834.6	TSL:1	c.-111-1468G>A		intron	N/A	ENSP00000398560.2	Q96N96-6
	ENSG00000273167	ENST00000382141.4	TSL:5	n.-111-1468G>A		intron	N/A	ENSP00000371576.4	A0A0A0MRY4

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43259 AN: 151956 Hom.: 6528 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.285 AC: 43278 AN: 152074 Hom.: 6530 Cov.: 32 AF XY: 0.288 AC XY: 21399 AN XY: 74312

African (AFR) AF: 0.193 AC: 7991 AN: 41472

American (AMR) AF: 0.248 AC: 3790 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 1313 AN: 3470

East Asian (EAS) AF: 0.503 AC: 2599 AN: 5172

South Asian (SAS) AF: 0.354 AC: 1708 AN: 4822

European-Finnish (FIN) AF: 0.303 AC: 3197 AN: 10558

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.320 AC: 21728 AN: 67988

Other (OTH) AF: 0.283 AC: 597 AN: 2112

Alfa AF: 0.298 Hom.: 10057

Bravo AF: 0.273

Asia WGS AF: 0.381 AC: 1323 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.8
DANN	Benign	0.83
PhyloP100		0.10
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: rs715921; hg19: chr13-24795489;