rs10192428

Variant names:

• chr2-231014025-G-A
• rs10192428
• XR_001738627.3:n.1070G>A

Variant summary

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

The XR_001738627.3(SPATA3):​n.1070G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.437 in 151,604 control chromosomes in the GnomAD database, including 15,572 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 0.44 (15572 hom., cov: 29)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: SPATA3 XR_001738627.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.586
• Publications: 4 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.587 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATA3	ENST00000452881.5	TSL:2	c.*378G>A		3_prime_UTR	Exon 6 of 9	ENSP00000388895.1
	SPATA3	ENST00000455816.1	TSL:5	c.*146+1328G>A		intron	N/A	ENSP00000388741.1
	SPATA3	ENST00000495639.1	TSL:3	c.*39-5695G>A		intron	N/A	ENSP00000436378.1

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66104 AN: 151482 Hom.: 15540 Cov.: 29

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.415

GnomAD4 exome AF: 0.500 AC: 2 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 2 AN XY: 4

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 2 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.437 AC: 66189 AN: 151600 Hom.: 15572 Cov.: 29 AF XY: 0.439 AC XY: 32527 AN XY: 74072

African (AFR) AF: 0.594 AC: 24514 AN: 41304

American (AMR) AF: 0.496 AC: 7554 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 875 AN: 3468

East Asian (EAS) AF: 0.475 AC: 2447 AN: 5148

South Asian (SAS) AF: 0.483 AC: 2320 AN: 4806

European-Finnish (FIN) AF: 0.378 AC: 3955 AN: 10474

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.341 AC: 23127 AN: 67858

Other (OTH) AF: 0.414 AC: 872 AN: 2104

Alfa AF: 0.414 Hom.: 2850

Bravo AF: 0.451

Asia WGS AF: 0.543 AC: 1887 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.8
DANN	Benign	0.75
PhyloP100		-0.59
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: rs10192428; hg19: chr2-231878740;