chr13-24119603-G-A

Variant names:

• chr13-24119603-G-A
• rs2104257
• ENST00000424834.6:c.-112+101902G>A

Variant summary

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

The ENST00000424834.6(SPATA13):​c.-112+101902G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0822 in 152,184 control chromosomes in the GnomAD database, including 708 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 0.082 (708 hom., cov: 32)
• Consequence: SPATA13 ENST00000424834.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.778
• Publications: 4 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPATA13	NM_001286792.2	c.75+101902G>A		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+101902G>A		intron_variant	Intron 3 of 14	1		ENSP00000398560.2
ENSG00000273167	ENST00000382141.4	n.-112+101902G>A		intron_variant	Intron 3 of 15	5		ENSP00000371576.4

Frequencies

GnomAD3 genomes AF: 0.0824 AC: 12524 AN: 152066 Hom.: 708 Cov.: 32

Gnomad AFR AF: 0.0218

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.0581

Gnomad ASJ AF: 0.0608

Gnomad EAS AF: 0.000771

Gnomad SAS AF: 0.0884

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.0764

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

GnomAD4 genome AF: 0.0822 AC: 12515 AN: 152184 Hom.: 708 Cov.: 32 AF XY: 0.0810 AC XY: 6024 AN XY: 74392

African (AFR) AF: 0.0217 AC: 902 AN: 41538

American (AMR) AF: 0.0581 AC: 888 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0608 AC: 211 AN: 3468

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5178

South Asian (SAS) AF: 0.0885 AC: 427 AN: 4826

European-Finnish (FIN) AF: 0.125 AC: 1325 AN: 10566

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8493 AN: 67994

Other (OTH) AF: 0.0747 AC: 158 AN: 2116

Alfa AF: 0.0941 Hom.: 157

Bravo AF: 0.0730

Asia WGS AF: 0.0320 AC: 113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.95
DANN	Benign	0.68
PhyloP100		-0.78
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: rs2104257; hg19: chr13-24693742;