chr13-24209049-C-T

Variant names:

• chr13-24209049-C-T
• rs7331042
• NM_001166271.3:c.-111-13770C>T

Variant summary

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

The NM_001166271.3(SPATA13):​c.-111-13770C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 152,054 control chromosomes in the GnomAD database, including 9,541 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 0.32 (9541 hom., cov: 32)
• Consequence: SPATA13 NM_001166271.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPATA13	NM_001166271.3	c.-111-13770C>T		intron_variant	Intron 1 of 12	ENST00000382108.8	NP_001159743.1
SPATA13	NM_001286792.2	c.76-13770C>T		intron_variant	Intron 3 of 14		NP_001273721.1
SPATA13	NM_153023.4	c.-222-40428C>T		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.-111-13770C>T		intron_variant	Intron 1 of 12	5	NM_001166271.3	ENSP00000371542.3
ENSG00000273167	ENST00000382141.4	n.-111-13770C>T		intron_variant	Intron 3 of 15	5		ENSP00000371576.4

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48997 AN: 151936 Hom.: 9529 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.628

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.322 AC: 49031 AN: 152054 Hom.: 9541 Cov.: 32 AF XY: 0.332 AC XY: 24652 AN XY: 74320

African (AFR) AF: 0.123 AC: 5101 AN: 41482

American (AMR) AF: 0.501 AC: 7660 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.348 AC: 1208 AN: 3468

East Asian (EAS) AF: 0.629 AC: 3234 AN: 5144

South Asian (SAS) AF: 0.491 AC: 2364 AN: 4818

European-Finnish (FIN) AF: 0.343 AC: 3624 AN: 10568

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.365 AC: 24816 AN: 67980

Other (OTH) AF: 0.330 AC: 696 AN: 2112

Alfa AF: 0.344 Hom.: 1247

Bravo AF: 0.326

Asia WGS AF: 0.490 AC: 1702 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.14
DANN	Benign	0.40
PhyloP100		-1.3
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: rs7331042; hg19: chr13-24783187;