rs4973374

Positions:

• chr2-231020700-T-C
• chr2-231020700-T-G

Variant summary

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

The ENST00000452881.5(SPATA3):​c.*733+813T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.622 in 151,996 control chromosomes in the GnomAD database, including 30,147 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 0.62 (30147 hom., cov: 32)
• Consequence: SPATA3 ENST00000452881.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.648

Genes affected

SPATA3 (HGNC:17884): (spermatogenesis associated 3) Predicted to be integral component of 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.757 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPATA3	ENST00000452881.5	c.*733+813T>C		intron_variant		2		ENSP00000388895	P1
SPATA3	ENST00000455816.1	c.*147-4279T>C		intron_variant		5		ENSP00000388741	P1
SPATA3	ENST00000495639.1	c.*206+813T>C		intron_variant		3		ENSP00000436378

Frequencies

GnomAD3 genomes AF: 0.622 AC: 94441 AN: 151878 Hom.: 30100 Cov.: 32

Gnomad AFR AF: 0.764

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.622 AC: 94541 AN: 151996 Hom.: 30147 Cov.: 32 AF XY: 0.621 AC XY: 46175 AN XY: 74300

Gnomad4 AFR AF: 0.764

Gnomad4 AMR AF: 0.596

Gnomad4 ASJ AF: 0.477

Gnomad4 EAS AF: 0.709

Gnomad4 SAS AF: 0.595

Gnomad4 FIN AF: 0.577

Gnomad4 NFE AF: 0.555

Gnomad4 OTH AF: 0.565

Alfa AF: 0.544 Hom.: 13322

Bravo AF: 0.628

Asia WGS AF: 0.679 AC: 2360 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.0
DANN	Benign	0.71

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4973374; hg19: chr2-231885415;