2-231020700-T-C

Variant names:

• chr2-231020700-T-C
• rs4973374
• ENST00000452881.5:c.*733+813T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

SPATA3 (HGNC:17884): (spermatogenesis associated 3) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

SPATA3 Gene-Disease associations (from GenCC):

• male infertility with azoospermia or oligozoospermia due to single gene mutation

  Inheritance: AR Classification: MODERATE Submitted by: King Faisal Specialist Hospital and Research Center

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000452881.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATA3	ENST00000452881.5	TSL:2	c.*733+813T>C		intron	N/A	ENSP00000388895.1
	SPATA3	ENST00000455816.1	TSL:5	c.*147-4279T>C		intron	N/A	ENSP00000388741.1
	SPATA3	ENST00000495639.1	TSL:3	c.*206+813T>C		intron	N/A	ENSP00000436378.1

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

African (AFR) AF: 0.764 AC: 31691 AN: 41478

American (AMR) AF: 0.596 AC: 9086 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.477 AC: 1655 AN: 3470

East Asian (EAS) AF: 0.709 AC: 3664 AN: 5170

South Asian (SAS) AF: 0.595 AC: 2862 AN: 4814

European-Finnish (FIN) AF: 0.577 AC: 6077 AN: 10540

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.555 AC: 37718 AN: 67960

Other (OTH) AF: 0.565 AC: 1192 AN: 2110

Alfa AF: 0.549 Hom.: 19255

Bravo AF: 0.628

Asia WGS AF: 0.679 AC: 2360 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.0
DANN	Benign	0.71
PhyloP100		-0.65
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs4973374; hg19: chr2-231885415;