rs17079928

Variant names:

• chr13-24080089-G-A
• rs17079928
• ENST00000424834.6:c.-112+62388G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001286792.2(SPATA13):​c.75+62388G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 152,162 control chromosomes in the GnomAD database, including 6,090 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 (6090 hom., cov: 33)
• Consequence: SPATA13 NM_001286792.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.335

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]

ENSG00000273167 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.304 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPATA13	NM_001286792.2	c.75+62388G>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+62388G>A		intron_variant	Intron 3 of 14	1		ENSP00000398560.2
ENSG00000273167	ENST00000382141.4	n.-112+62388G>A		intron_variant	Intron 3 of 15	5		ENSP00000371576.4

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42394 AN: 152044 Hom.: 6075 Cov.: 33

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.199

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.0967

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.279 AC: 42435 AN: 152162 Hom.: 6090 Cov.: 33 AF XY: 0.274 AC XY: 20362 AN XY: 74384

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.262

Gnomad4 ASJ AF: 0.344

Gnomad4 EAS AF: 0.0963

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.308

Gnomad4 OTH AF: 0.290

Alfa AF: 0.303 Hom.: 12502

Bravo AF: 0.279

Asia WGS AF: 0.110 AC: 385 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	2.3
DANN	Benign	0.50

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

Publications

LitVar

Other links and lift over

dbSNP: rs17079928; hg19: chr13-24654228; COSMIC: COSV66150415;