rs2793483

Positions:

• chr13-24185549-G-A

Variant summary

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

The NM_001166271.3(SPATA13):​c.-112+24617G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.642 in 152,026 control chromosomes in the GnomAD database, including 31,373 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 0.64 (31373 hom., cov: 32)
• Consequence: SPATA13 NM_001166271.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.11

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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.65 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPATA13	NM_001166271.3	c.-112+24617G>A		intron_variant		ENST00000382108.8
SPATA13	NM_001286792.2	c.76-37270G>A		intron_variant
SPATA13	NM_153023.4	c.-223+24617G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPATA13	ENST00000382108.8	c.-112+24617G>A		intron_variant		5	NM_001166271.3
SPATA13	ENST00000424834.6	c.-111-37270G>A		intron_variant		1
SPATA13	ENST00000382095.8	c.-223+24617G>A		intron_variant		2
SPATA13	ENST00000466831.2	n.211+24617G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.642 AC: 97469 AN: 151908 Hom.: 31338 Cov.: 32

Gnomad AFR AF: 0.651

Gnomad AMI AF: 0.716

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.655

Gnomad OTH AF: 0.642

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

GnomAD4 genome AF: 0.642 AC: 97547 AN: 152026 Hom.: 31373 Cov.: 32 AF XY: 0.639 AC XY: 47463 AN XY: 74312

Gnomad4 AFR AF: 0.651

Gnomad4 AMR AF: 0.543

Gnomad4 ASJ AF: 0.662

Gnomad4 EAS AF: 0.580

Gnomad4 SAS AF: 0.651

Gnomad4 FIN AF: 0.670

Gnomad4 NFE AF: 0.655

Gnomad4 OTH AF: 0.645

Alfa AF: 0.649 Hom.: 20798

Bravo AF: 0.630

Asia WGS AF: 0.657 AC: 2282 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.0020
DANN	Benign	0.49

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: rs2793483; hg19: chr13-24759688;