13-24187906-A-C

Position:

• chr13-24187906-A-C

Variant summary

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

The NM_001166271.3(SPATA13):​c.-112+26974A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.734 in 152,132 control chromosomes in the GnomAD database, including 45,622 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 0.73 (45622 hom., cov: 32)
• Consequence: SPATA13 NM_001166271.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.564

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=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.903 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SPATA13	NM_001166271.3	c.-112+26974A>C		intron_variant		ENST00000382108.8	NP_001159743.1
SPATA13	NM_001286792.2	c.76-34913A>C		intron_variant			NP_001273721.1
SPATA13	NM_153023.4	c.-223+26974A>C		intron_variant			NP_694568.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPATA13	ENST00000382108.8	c.-112+26974A>C		intron_variant		5	NM_001166271.3	ENSP00000371542
SPATA13	ENST00000424834.6	c.-111-34913A>C		intron_variant		1		ENSP00000398560
SPATA13	ENST00000382095.8	c.-223+26974A>C		intron_variant		2		ENSP00000371527
SPATA13	ENST00000466831.2	n.211+26974A>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.734 AC: 111643 AN: 152014 Hom.: 45617 Cov.: 32

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.918

Gnomad AMR AF: 0.826

Gnomad ASJ AF: 0.868

Gnomad EAS AF: 0.704

Gnomad SAS AF: 0.776

Gnomad FIN AF: 0.923

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.909

Gnomad OTH AF: 0.782

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

GnomAD4 genome AF: 0.734 AC: 111673 AN: 152132 Hom.: 45622 Cov.: 32 AF XY: 0.736 AC XY: 54743 AN XY: 74394

Gnomad4 AFR AF: 0.346

Gnomad4 AMR AF: 0.825

Gnomad4 ASJ AF: 0.868

Gnomad4 EAS AF: 0.704

Gnomad4 SAS AF: 0.776

Gnomad4 FIN AF: 0.923

Gnomad4 NFE AF: 0.909

Gnomad4 OTH AF: 0.784

Alfa AF: 0.810 Hom.: 7203

Bravo AF: 0.709

Asia WGS AF: 0.741 AC: 2578 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.34

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: rs9511117; hg19: chr13-24762045;