2-231015397-G-A

Variant names:

• chr2-231015397-G-A
• rs6750230
• ENST00000452881.5:c.*565+1185G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000452881.5(SPATA3):​c.*565+1185G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 151,546 control chromosomes in the GnomAD database, including 12,943 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 0.40 (12943 hom., cov: 30)
• Consequence: SPATA3 ENST00000452881.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.54 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATA3	ENST00000452881.5	TSL:2	c.*565+1185G>A		intron	N/A	ENSP00000388895.1
	SPATA3	ENST00000455816.1	TSL:5	c.*146+2700G>A		intron	N/A	ENSP00000388741.1
	SPATA3	ENST00000495639.1	TSL:3	c.*39-4323G>A		intron	N/A	ENSP00000436378.1

Frequencies

GnomAD3 genomes AF: 0.399 AC: 60350 AN: 151428 Hom.: 12912 Cov.: 30

Gnomad AFR AF: 0.546

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.404

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.399 AC: 60424 AN: 151546 Hom.: 12943 Cov.: 30 AF XY: 0.398 AC XY: 29475 AN XY: 73992

African (AFR) AF: 0.546 AC: 22531 AN: 41264

American (AMR) AF: 0.449 AC: 6831 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.242 AC: 838 AN: 3466

East Asian (EAS) AF: 0.343 AC: 1759 AN: 5126

South Asian (SAS) AF: 0.299 AC: 1434 AN: 4800

European-Finnish (FIN) AF: 0.356 AC: 3730 AN: 10484

Middle Eastern (MID) AF: 0.421 AC: 122 AN: 290

European-Non Finnish (NFE) AF: 0.325 AC: 22052 AN: 67874

Other (OTH) AF: 0.378 AC: 795 AN: 2104

Alfa AF: 0.343 Hom.: 6680

Bravo AF: 0.415

Asia WGS AF: 0.358 AC: 1243 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.70
PhyloP100		-0.83
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: rs6750230; hg19: chr2-231880112;