rs17079773

chr13-24024245-C-T

Variant summary

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

The ENST00000424834.6(SPATA13):c.-112+6544C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,124 control chromosomes in the GnomAD database, including 1,475 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 0.12 (1475 hom., cov: 32)
• Consequence: SPATA13 ENST00000424834.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.832

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.423 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPATA13	NM_001286792.2	c.75+6544C>T		intron_variant
SPATA13	NR_104595.2	n.365+6544C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPATA13	ENST00000424834.6	c.-112+6544C>T		intron_variant		1
SPATA13	ENST00000439928.2	n.357+6544C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17998 AN: 152006 Hom.: 1478 Cov.: 32

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.0755

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.0328

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0802

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.118 AC: 17995 AN: 152124 Hom.: 1475 Cov.: 32 AF XY: 0.120 AC XY: 8915 AN XY: 74360

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.155

Gnomad4 ASJ AF: 0.0755

Gnomad4 EAS AF: 0.438

Gnomad4 SAS AF: 0.177

Gnomad4 FIN AF: 0.0328

Gnomad4 NFE AF: 0.0802

Gnomad4 OTH AF: 0.112

Alfa AF: 0.0979 Hom.: 1377

Bravo AF: 0.127

Asia WGS AF: 0.277 AC: 960 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	2.3
Dann	Benign	0.56

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: rs17079773; hg19: chr13-24598384; COSMIC: COSV66150128;