chr13-24084217-G-T

Position:

• chr13-24084217-G-T

Variant summary

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

The NM_001286792.2(SPATA13):​c.75+66516G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.632 in 151,954 control chromosomes in the GnomAD database, including 30,788 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 0.63 (30788 hom., cov: 32)
• Consequence: SPATA13 NM_001286792.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.259

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 (AFR) allele frequency at 95% confidence interval = 0.741 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SPATA13	NM_001286792.2	c.75+66516G>T		intron_variant			NP_001273721.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPATA13	ENST00000424834.6	c.-112+66516G>T		intron_variant		1		ENSP00000398560.2
ENSG00000273167	ENST00000382141.4	n.-112+66516G>T		intron_variant		5		ENSP00000371576.4

Frequencies

GnomAD3 genomes AF: 0.631 AC: 95874 AN: 151836 Hom.: 30733 Cov.: 32

Gnomad AFR AF: 0.747

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.636

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.586

Gnomad OTH AF: 0.621

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

GnomAD4 genome AF: 0.632 AC: 95989 AN: 151954 Hom.: 30788 Cov.: 32 AF XY: 0.632 AC XY: 46923 AN XY: 74248

Gnomad4 AFR AF: 0.748

Gnomad4 AMR AF: 0.596

Gnomad4 ASJ AF: 0.666

Gnomad4 EAS AF: 0.539

Gnomad4 SAS AF: 0.637

Gnomad4 FIN AF: 0.576

Gnomad4 NFE AF: 0.586

Gnomad4 OTH AF: 0.624

Alfa AF: 0.607 Hom.: 28608

Bravo AF: 0.638

Asia WGS AF: 0.621 AC: 2163 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	0.60
DANN	Benign	0.74

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs9805786; hg19: chr13-24658356;